Contacts of the helix formed by residues 99 - 120 (chain C) in PDB entry 3UGV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ALA* 1.3 73.9 - - - +
100C LEU* 1.3 66.7 + - - -
101C SER 3.2 3.8 + - - -
102C MET* 3.2 3.8 + - - +
103C ILE* 3.2 27.6 + - - +
257C TYR* 3.5 22.5 - - - -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ALA* 4.6 9.6 - - + -
62C TYR* 4.0 35.2 - - + -
63C LEU* 3.6 39.1 - - + +
98C ALA 3.9 0.6 + - - -
99C GLY* 1.3 71.9 - - - -
101C SER* 1.3 62.2 + - - +
103C ILE* 3.3 14.9 + - + +
104C ALA* 3.0 20.4 + - - +
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Residues in contact with SER 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C MET* 4.2 3.8 - - - +
89C ARG* 6.0 3.1 - - - -
92C LEU* 3.5 37.7 - - - -
95C VAL* 3.9 9.5 + - - -
96C GLY 2.5 29.4 + - - -
97C TYR* 4.1 0.8 + - - -
98C ALA 3.2 10.2 + - - -
100C LEU* 1.3 76.3 - - - +
102C MET* 1.3 60.0 + - - +
104C ALA* 3.3 5.4 + - - +
105C ALA* 3.1 22.6 + - - +
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Residues in contact with MET 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.5 21.5 - - - +
89C ARG* 3.4 34.8 - - - +
97C TYR 3.2 20.2 + - - +
99C GLY 3.2 9.0 + - - +
101C SER* 1.3 80.5 + - - +
103C ILE* 1.3 57.1 + - - +
105C ALA* 3.2 6.2 + - - -
106C SER* 2.9 34.5 + - - -
257C TYR* 4.0 11.2 - - + -
258C GLY* 3.8 11.7 - - - +
279C MET 4.0 1.6 - - - +
280C ARG 3.2 33.0 - - - +
281C ILE 3.6 12.1 - - - +
282C GLY* 3.6 12.3 - - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.7 13.9 - - + +
54C PRO* 5.2 2.2 - - + +
63C LEU* 3.7 27.6 - - + -
99C GLY 3.2 16.7 + - - +
100C LEU* 3.4 20.9 - - + +
102C MET* 1.3 78.1 - - - +
104C ALA* 1.3 62.5 + - - +
106C SER* 3.4 2.1 + - - -
107C GLY 3.2 17.0 + - - -
257C TYR* 4.2 19.5 - - + +
279C MET* 3.3 56.5 - - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 4.9 1.8 - - - -
63C LEU* 4.2 9.8 - - + +
66C ALA* 4.3 18.8 - - + -
67C LEU* 3.4 18.4 - - + +
70C MET* 3.8 21.5 - - + -
100C LEU 3.0 13.1 + - - +
101C SER* 3.6 9.4 - - - +
102C MET 3.3 0.2 - - - -
103C ILE* 1.3 78.2 - - - +
105C ALA* 1.3 63.2 + - - +
106C SER 3.3 0.3 + - - -
107C GLY 3.3 0.9 + - - -
108C VAL* 3.2 24.6 + - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C MET* 4.1 4.4 - - + +
85C TYR* 5.0 6.6 - - + -
88C THR* 3.3 36.3 + - - +
89C ARG* 4.6 13.9 - - + +
101C SER 3.1 13.6 + - - +
102C MET* 3.2 14.3 + - - +
104C ALA* 1.3 75.8 - - - +
106C SER* 1.3 51.8 + - - +
108C VAL* 3.5 5.2 - - - +
109C ASP* 2.8 33.9 + - - +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C MET* 2.9 19.7 + - - -
103C ILE 3.7 1.3 - - - -
104C ALA 3.3 0.2 - - - -
105C ALA* 1.3 74.2 - - - +
107C GLY* 1.3 66.1 + - - +
109C ASP* 3.1 4.8 + - - +
110C MET* 2.9 31.2 + - - +
278C PHE 3.4 17.3 - - - -
279C MET* 3.0 28.0 + - - -
282C GLY* 3.0 24.0 + - - -
283C GLY* 3.5 7.4 - - - +
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Residues in contact with GLY 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 3.5 29.8 - - - +
50C ALA* 4.6 1.4 - - - +
51C TYR 5.8 0.2 - - - -
52C LEU* 3.7 20.7 - - - +
103C ILE 3.2 8.3 + - - -
104C ALA 3.3 3.3 + - - -
106C SER* 1.3 79.6 - - - +
108C VAL* 1.3 61.3 + - - +
110C MET* 3.3 7.2 + - - +
111C ALA* 3.2 17.8 + - - +
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 5.4 0.2 - - + -
10C LEU* 3.9 24.0 - - + -
38C ILE* 4.2 1.2 - - - +
40C ILE* 5.3 0.2 - - + -
67C LEU* 3.7 16.8 - - + -
70C MET* 4.1 21.1 - - + -
74C LEU* 4.2 12.1 - - + -
84C ILE* 4.0 20.9 - - + -
88C THR* 4.6 2.7 - - + -
104C ALA 3.2 14.6 + - - +
105C ALA* 3.5 9.0 - - - +
107C GLY* 1.3 75.7 - - - +
109C ASP* 1.3 62.7 + - - +
110C MET 3.2 0.2 + - - -
111C ALA* 3.2 3.2 + - - +
112C VAL* 2.9 38.6 + - + +
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 4.0 9.9 - - - +
84C ILE* 6.1 1.6 - - - -
85C TYR* 3.8 12.7 - - + -
105C ALA 2.8 22.3 + - - +
106C SER* 3.1 10.9 + - - +
108C VAL* 1.3 74.8 - - - +
110C MET* 1.3 57.7 + - - +
112C VAL* 3.9 5.5 - - - +
113C TRP* 3.0 34.3 + - - -
282C GLY 3.8 8.7 - - - +
284C VAL 2.8 28.9 + - - -
285C SER* 2.5 34.3 + - - -
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Residues in contact with MET 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ALA* 3.7 16.4 - - + +
51C TYR 3.8 13.9 - - - +
52C LEU* 3.8 26.7 - - + -
106C SER 2.9 22.2 + - - +
107C GLY* 3.8 3.4 - - - +
108C VAL 3.2 0.2 - - - -
109C ASP* 1.3 75.7 - - - +
111C ALA* 1.3 59.2 + - - +
113C TRP* 3.4 2.6 + - - +
114C ASP* 3.0 28.4 + - - +
124C LEU* 5.8 0.5 - - - +
278C PHE* 4.0 27.1 - - + +
283C GLY* 3.9 14.6 - - - -
284C VAL* 4.3 16.1 - - + +
306C TYR* 4.0 13.5 - - + -
309C VAL* 3.8 27.4 - - + -
352C LEU* 4.5 4.2 - - + +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 3.8 17.9 - - + -
40C ILE* 3.4 25.6 - - + -
48C GLY* 3.6 10.2 - - - +
49C ARG 4.5 0.4 - - - -
50C ALA* 3.5 20.3 - - + +
107C GLY 3.2 10.0 + - - +
108C VAL 3.2 6.6 + - - +
110C MET* 1.3 76.9 - - - +
112C VAL* 1.3 57.4 + - - +
114C ASP* 3.1 6.8 + - - +
115C ALA* 2.8 24.8 + - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.9 2.0 - - + -
40C ILE* 4.2 11.4 - - + -
79C LEU* 3.7 25.1 - - + +
81C PRO* 3.6 37.5 - - + -
84C ILE* 4.1 17.9 - - + -
108C VAL* 2.9 36.2 + - + +
109C ASP* 3.9 5.2 - - - +
111C ALA* 1.3 75.8 - - - +
113C TRP* 1.3 65.3 + - - +
115C ALA* 3.3 7.8 + - - +
116C LEU* 3.0 21.7 + - - +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 3.2 29.2 - - + +
82C ALA* 5.1 6.1 - - + -
109C ASP* 3.0 41.6 + - - +
110C MET 3.9 3.4 - - - +
112C VAL* 1.3 75.5 - - - +
114C ASP* 1.3 62.9 + - - +
116C LEU* 3.2 14.0 + - + +
117C ALA* 3.1 23.0 + - - +
124C LEU* 4.2 18.0 - - + +
127C LEU* 3.7 32.3 - - + -
128C LEU* 3.8 18.2 - - + -
284C VAL* 3.5 27.8 - - + -
285C SER* 2.9 31.1 + - - +
288C MET* 6.0 2.2 - - + -
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLY* 3.2 4.2 - - - -
49C ARG* 2.7 40.7 + - - +
110C MET 3.0 14.5 + - - +
111C ALA 3.3 8.5 - - - +
113C TRP* 1.3 77.2 - - - +
115C ALA* 1.3 60.9 + - - +
117C ALA* 3.2 3.9 + - - +
118C ARG* 3.0 44.5 + - - +
124C LEU* 5.3 2.8 - - - +
351C GLY* 3.2 9.1 - - - -
352C LEU* 2.6 43.2 + - + +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.3 0.4 - - - +
40C ILE* 4.6 4.9 - - + -
42C THR* 4.9 3.8 - - + -
46C VAL* 3.5 11.4 - - + +
47C PRO 3.5 23.3 - - - +
48C GLY* 3.8 7.0 - - - +
79C LEU* 3.5 28.3 - - + -
111C ALA 2.8 16.7 + - - +
112C VAL* 3.6 4.5 - - - +
113C TRP 3.3 0.2 - - - -
114C ASP* 1.3 73.4 + - - +
116C LEU* 1.3 58.3 + - - +
118C ARG 3.2 1.2 + - - -
119C ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.0 22.9 - - + -
79C LEU* 4.1 13.8 - - + +
80C ALA* 5.7 0.2 - - - -
81C PRO* 4.0 24.7 - - + -
112C VAL 3.0 14.6 + - - +
113C TRP* 3.2 27.1 + - + +
115C ALA* 1.3 76.7 - - - +
117C ALA* 1.3 62.0 + - - +
119C ALA* 3.6 2.7 + - + +
120C ALA* 3.3 21.0 + - - +
127C LEU* 4.1 14.3 - - + +
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C TRP 3.1 12.6 + - - +
114C ASP 3.7 2.7 - - - +
116C LEU* 1.3 75.3 - - - +
118C ARG* 1.3 65.6 + - - +
120C ALA* 3.2 4.6 + - - +
121C ASN 3.0 3.5 + - - -
122C MET 2.9 43.9 + - - +
123C PRO 4.4 0.2 - - - -
124C LEU* 4.0 18.2 - - + -
127C LEU* 4.1 15.9 - - + -
351C GLY* 3.6 17.0 - - - -
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Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 3.8 10.5 - - + -
47C PRO* 3.1 34.5 + - + +
48C GLY* 4.8 0.2 - - - -
49C ARG* 3.7 22.0 - - - +
114C ASP* 3.0 36.9 + - - +
115C ALA 3.2 7.2 + - - +
117C ALA* 1.3 77.6 - - - +
119C ALA* 1.3 54.2 + - - +
121C ASN* 2.6 26.9 + - - +
350C PRO* 4.1 28.9 + - + +
351C GLY* 4.1 10.1 - - - +
353C GLY* 4.0 9.1 - - - +
354C LEU* 3.2 37.8 + - - +
355C ASP* 5.0 2.0 + - - -
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.6 32.5 - - + -
46C VAL* 3.8 20.9 - - + +
115C ALA 2.9 10.2 + - - +
116C LEU* 3.8 6.3 - - + +
118C ARG* 1.3 75.3 - - - +
120C ALA* 1.3 59.2 + - - +
121C ASN* 3.2 1.7 + - - +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.3 13.9 + - + +
117C ALA 3.2 5.5 + - - +
118C ARG 3.1 0.8 - - - -
119C ALA* 1.3 77.6 - - - +
121C ASN* 1.3 70.5 + - - +
122C MET* 3.4 23.5 + - + +
127C LEU* 4.2 19.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il