Contacts of the helix formed by residues 99 - 120 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 1.3 71.7 - - - +
100D LEU* 1.3 66.6 + - - -
101D SER 3.2 2.9 - - - -
102D MET* 3.0 16.5 + - - +
103D ILE* 3.1 23.7 + - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ALA* 4.7 13.0 - - + -
62D TYR* 4.1 27.4 - - + -
63D LEU* 3.7 40.4 - - + +
98D ALA 3.9 1.0 + - - -
99D GLY* 1.3 70.8 - - - -
101D SER* 1.3 61.1 + - - +
103D ILE* 3.2 14.5 + - + +
104D ALA* 3.1 21.1 + - - +
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D MET* 4.2 3.8 - - - +
89D ARG* 6.0 2.2 - - - -
92D LEU* 3.5 36.3 - - - +
95D VAL* 3.5 17.0 + - - +
96D GLY 2.9 29.0 + - - -
97D TYR* 4.3 2.7 - - - -
98D ALA 4.3 2.2 + - - -
99D GLY 3.1 0.6 + - - -
100D LEU* 1.3 77.7 - - - +
102D MET* 1.3 64.9 + - - +
104D ALA* 3.3 3.9 + - - +
105D ALA* 3.2 21.6 + - - +
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Residues in contact with MET 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D TYR* 3.4 29.6 - - - +
89D ARG* 3.4 35.4 - - - +
97D TYR 3.2 17.9 + - - +
98D ALA* 4.4 2.2 - - - -
99D GLY 3.0 15.0 + - - +
101D SER* 1.3 78.3 - - - +
103D ILE* 1.3 60.5 + - + +
105D ALA* 3.2 6.3 + - - +
106D SER* 2.8 46.9 + - - +
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.6 22.0 - - + +
54D PRO* 5.1 9.9 - - + -
63D LEU* 4.0 24.2 - - + -
99D GLY* 3.1 22.6 + - - +
100D LEU* 3.5 19.7 - - + +
101D SER 3.2 0.4 - - - -
102D MET* 1.3 79.6 - - + +
104D ALA* 1.3 61.7 + - - +
106D SER* 3.4 8.1 + - - -
107D GLY 3.2 16.5 + - - -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 4.8 2.5 - - - -
63D LEU* 4.1 8.7 - - + +
66D ALA* 4.2 21.3 - - + -
67D LEU* 3.5 23.1 - - + +
70D MET* 3.6 23.6 - - + -
92D LEU* 5.3 0.2 - - + -
100D LEU 3.1 11.6 + - - +
101D SER* 3.7 5.2 - - - +
103D ILE* 1.3 76.9 - - - +
105D ALA* 1.3 63.8 + - - +
107D GLY 3.3 2.3 + - - -
108D VAL* 3.2 19.8 + - - +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D MET* 3.8 10.0 - - + +
85D TYR* 4.8 8.1 - - + -
88D THR* 3.5 29.3 + - - +
89D ARG* 4.4 16.8 - - + +
101D SER 3.2 11.0 + - - +
102D MET* 3.2 14.1 + - - +
104D ALA* 1.3 78.4 - - - +
106D SER* 1.3 57.1 + - - +
108D VAL* 3.6 4.4 + - - +
109D ASP* 3.0 27.4 + - - +
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 5.0 2.7 - - - -
85D TYR* 5.3 4.2 - - - -
102D MET* 2.8 33.5 + - - +
103D ILE* 3.6 8.3 - - - -
104D ALA 3.2 0.2 - - - -
105D ALA* 1.3 76.5 - - - +
107D GLY* 1.3 62.9 + - - +
109D ASP* 3.4 7.2 + - - +
110D MET* 3.1 37.7 + - - +
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Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.5 30.3 - - - +
50D ALA* 4.8 1.4 - - - +
51D TYR 5.6 0.2 - - - -
52D LEU* 3.8 19.2 - - - +
103D ILE 3.2 8.9 + - - -
104D ALA 3.3 2.8 + - - -
106D SER* 1.3 75.8 - - - +
108D VAL* 1.3 66.1 + - - +
110D MET* 3.6 6.4 + - - +
111D ALA* 3.4 17.3 + - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 5.4 0.2 - - + -
10D LEU* 3.9 28.5 - - + -
38D ILE* 4.3 0.8 - - - +
67D LEU* 3.9 7.2 - - + -
70D MET* 3.9 26.5 - - + -
74D LEU* 4.1 9.6 - - + -
84D ILE* 3.6 31.4 - - + -
88D THR* 4.5 2.0 - - + -
104D ALA 3.2 14.7 + - - +
105D ALA* 3.7 8.5 - - - +
107D GLY* 1.3 76.1 - - - +
109D ASP* 1.3 57.7 + - - +
111D ALA* 3.2 3.9 + - - +
112D VAL* 2.9 42.9 + - + +
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Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 4.0 7.3 - - - +
84D ILE* 6.0 0.9 - - - -
85D TYR* 4.0 32.7 + - + +
105D ALA 3.0 18.5 + - - +
106D SER* 3.6 8.7 - - - +
107D GLY 3.3 0.4 - - - -
108D VAL* 1.3 78.1 - - - +
110D MET* 1.3 67.0 + - - +
112D VAL* 3.4 7.0 + - - +
113D TRP* 3.0 55.8 + - - -
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Residues in contact with MET 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ALA* 3.7 17.6 - - + +
51D TYR 3.7 23.3 - - - +
52D LEU* 3.8 19.7 - - + -
106D SER* 3.1 23.5 + - - +
107D GLY* 4.1 4.3 - - - +
109D ASP* 1.3 84.0 - - - +
111D ALA* 1.3 59.3 + - - +
113D TRP* 3.6 5.7 + - - +
114D ASP* 3.1 24.6 + - - +
124D LEU* 5.7 2.3 - - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.9 15.7 - - + -
40D ILE* 3.7 25.6 - - + -
48D GLY* 3.7 7.9 - - - -
49D ARG 4.4 3.8 - - - +
50D ALA* 3.7 19.9 - - + +
107D GLY 3.4 13.7 + - - +
108D VAL 3.2 3.4 + - - +
110D MET* 1.3 77.9 - - - +
112D VAL* 1.3 59.2 + - - +
114D ASP* 3.1 7.4 + - - +
115D ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 4.9 1.3 - - + -
40D ILE* 3.2 21.8 - - + -
79D LEU* 3.5 33.4 - - + +
81D PRO* 3.5 33.9 - - + +
84D ILE* 4.1 12.3 - - + -
108D VAL* 2.9 32.2 + - + +
109D ASP* 3.4 15.5 - - - +
111D ALA* 1.3 73.7 - - - +
113D TRP* 1.3 64.0 + - - +
115D ALA* 3.2 1.9 + - - +
116D LEU* 2.9 26.0 + - - +
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Residues in contact with TRP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 3.2 34.8 - - + +
82D ALA* 5.1 7.0 - - + -
109D ASP* 3.0 48.0 + - - +
110D MET* 3.9 6.3 - - - +
112D VAL* 1.3 74.8 - - - +
114D ASP* 1.3 65.9 + - - +
116D LEU* 3.9 13.2 - - + +
117D ALA* 3.1 24.4 + - - +
124D LEU* 3.8 25.5 - - + +
127D LEU* 3.7 30.2 - - + +
128D LEU* 3.8 24.9 - - + -
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY* 3.5 2.8 - - - -
49D ARG* 2.8 40.1 + - - +
110D MET 3.1 14.8 + - - +
111D ALA 3.1 10.1 + - - +
113D TRP* 1.3 77.8 - - - +
115D ALA* 1.3 56.5 + - - +
117D ALA* 3.3 4.4 + - - +
118D ARG* 2.8 63.5 + - - +
124D LEU* 5.4 6.0 - - - +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.2 2.6 - - + +
40D ILE* 5.0 3.1 - - + -
42D THR* 4.9 4.5 - - + -
46D VAL* 3.6 12.2 - - + +
47D PRO 3.4 24.9 - - - +
48D GLY* 3.9 4.9 - - - +
79D LEU* 4.0 19.1 - - + -
111D ALA 3.0 12.0 + - - +
112D VAL* 3.2 9.2 + - - +
114D ASP* 1.3 78.0 + - - +
116D LEU* 1.3 55.4 + - - +
118D ARG* 3.4 0.4 + - - -
119D ALA* 2.8 30.4 + - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.1 21.5 - - + -
79D LEU* 4.4 9.4 - - + +
81D PRO* 3.9 25.8 - - + -
112D VAL 2.9 15.8 + - - +
113D TRP* 3.9 26.0 - - + +
114D ASP 3.3 0.4 - - - -
115D ALA* 1.3 75.5 - - - +
117D ALA* 1.3 62.4 + - - +
119D ALA* 3.2 6.1 + - + +
120D ALA* 3.1 22.1 + - + +
127D LEU* 4.1 14.1 - - + +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TRP 3.1 15.8 + - - +
114D ASP* 3.7 4.7 - - - +
116D LEU* 1.3 74.3 - - - +
118D ARG* 1.3 62.9 + - - +
120D ALA* 3.1 3.7 + - - +
121D ASN 3.1 3.1 + - - -
122D MET* 2.8 44.9 + - - +
124D LEU* 4.0 21.1 - - + +
127D LEU* 3.8 23.0 - - + +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 3.8 11.2 - - + -
47D PRO* 3.0 35.6 + - + +
49D ARG* 3.6 36.0 + - - +
114D ASP* 2.8 45.4 + - - +
115D ALA 3.6 4.7 - - - +
117D ALA* 1.3 75.8 - - + +
119D ALA* 1.3 55.7 + - - +
121D ASN* 2.7 28.4 + - - +
122D MET 4.1 1.5 + - - -
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 3.8 31.9 - - + -
46D VAL* 3.7 13.7 - - + +
115D ALA 2.8 18.1 + - - +
116D LEU* 3.5 8.7 - - + +
117D ALA 3.2 0.4 - - - -
118D ARG* 1.3 76.8 - - - +
120D ALA* 1.3 58.9 + - - +
121D ASN* 3.4 1.0 + - - +
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 3.1 12.1 + - + +
117D ALA 3.7 7.2 - - - +
118D ARG 3.1 1.0 - - - -
119D ALA* 1.3 75.4 - - - +
121D ASN* 1.3 70.3 + - - +
122D MET* 3.2 32.8 + - + +
127D LEU* 4.2 12.3 - - + -
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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
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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