Contacts of the helix formed by residues 103 - 119 (chain C) in PDB entry 2PCB
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 SER 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 3.3 15.8 + - - -
96C HIS* 4.4 2.9 - - - -
101C TRP 4.1 0.6 + - - -
102C ILE* 1.3 76.5 - - - +
104C SER* 1.3 54.6 + - - +
105C GLY 4.4 0.4 - - - -
106C ASP* 2.6 30.7 + - - +
107C LEU* 2.8 16.5 + - - +
130C ARG 2.8 28.5 + - - -
131C VAL* 4.5 1.1 - - - -
132C ASP* 3.5 22.9 - - - -
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY* 3.8 12.1 - - - -
72C ARG* 3.5 12.1 - - - +
96C HIS* 4.6 11.9 + - - -
102C ILE 4.3 0.2 + - - -
103C SER* 1.3 65.5 - - - +
105C GLY* 1.3 65.6 + - - -
106C ASP 3.0 1.6 - - - -
107C LEU* 4.5 5.4 - - - -
108C PHE* 2.9 61.7 + - - -
132C ASP* 2.6 29.3 + - - -
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Residues in contact with GLY 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ILE* 5.1 1.8 - - - -
66C SER* 3.4 25.9 - - - -
67C TYR 4.4 1.0 + - - -
69C GLY* 3.8 8.1 - - - +
103C SER* 3.3 1.6 - - - -
104C SER* 1.3 79.3 - - - +
106C ASP* 1.4 51.6 + - - +
108C PHE* 4.6 3.6 - - - -
109C SER* 2.7 31.4 + - - -
130C ARG* 2.9 22.1 - - - -
132C ASP* 3.6 4.6 + - - -
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Residues in contact with ASP 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 2.5 25.3 - - - +
102C ILE* 3.8 12.3 - - + -
103C SER* 2.6 31.3 + - - +
105C GLY* 1.4 67.5 - - - +
107C LEU* 1.3 53.3 + - - +
109C SER* 3.0 5.7 + - - -
110C LEU* 2.8 36.3 + - - +
126C TRP* 3.6 17.9 - - + -
128C CYS* 3.3 6.5 - - - +
129C GLY 3.2 17.2 + - - -
130C ARG* 2.5 45.2 + - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 4.3 14.8 - - + -
26C ILE* 4.7 3.4 - - + -
92C LEU* 4.3 30.4 - - + +
95C ILE* 3.7 28.3 - - + -
96C HIS* 3.1 46.0 - - + +
99C PHE* 6.0 0.2 - - + -
102C ILE* 4.0 14.0 - - + +
103C SER 2.8 16.4 + - - +
104C SER* 3.9 4.5 - - - +
106C ASP* 1.3 67.2 - - - +
108C PHE* 1.3 78.2 + - + +
109C SER 2.9 0.7 + - - -
110C LEU* 3.0 4.1 + - - +
111C GLY* 2.7 24.1 + - - -
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Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 4.2 19.4 - - + +
50C ALA* 3.4 12.8 + - - +
53C ILE* 3.8 35.7 - - + -
69C GLY* 4.5 5.8 - - - -
71C TYR* 4.3 16.4 - + + -
72C ARG* 4.4 9.6 - - + -
89C PHE* 3.7 39.0 - + - -
92C LEU* 3.6 22.2 - - + -
104C SER* 2.9 53.6 + - - +
105C GLY* 4.3 2.9 - - - -
107C LEU* 1.3 81.6 - - + +
109C SER* 1.3 59.8 + - - +
111C GLY* 3.7 1.1 + - - -
112C GLY 3.4 13.3 + - - -
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Residues in contact with SER 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ALA* 4.4 4.9 - - - -
53C ILE* 4.5 8.5 - - - -
66C SER* 4.8 1.1 - - - -
105C GLY 2.7 25.1 + - - -
106C ASP 3.0 9.0 + - - -
107C LEU 3.1 0.4 - - - -
108C PHE* 1.3 75.6 - - - +
110C LEU* 1.3 58.6 + - - +
112C GLY* 3.2 2.6 + - - -
113C VAL* 3.1 32.6 + - - +
126C TRP* 3.2 16.9 + - - -
130C ARG* 3.6 14.7 + - - -
270C LEU* 3.7 26.7 - - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 4.2 11.7 - - + +
22C VAL* 3.7 28.7 - - + -
23C TYR* 4.1 11.7 - - + +
26C ILE* 4.2 6.3 - - + -
102C ILE* 4.9 1.8 - - + -
106C ASP 2.8 18.4 + - - +
107C LEU* 3.8 4.5 - - - +
109C SER* 1.3 74.3 + - - +
111C GLY* 1.3 61.3 - - - +
113C VAL* 3.3 9.7 + - + +
114C THR* 2.5 43.7 + - - +
126C TRP* 4.2 28.3 - - + +
286C PHE* 3.5 33.4 - - + -
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 3.7 21.7 - - - +
46C LEU* 4.1 13.6 - - - +
49C LEU* 6.3 0.4 - - - -
92C LEU* 4.6 10.5 - - - -
107C LEU 2.7 18.7 + - - -
108C PHE* 4.2 1.6 - - - -
110C LEU* 1.3 73.7 - - - +
112C GLY* 1.3 63.6 + - - +
114C THR* 3.7 2.0 - - - -
115C ALA* 3.0 24.8 + - - +
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Residues in contact with GLY 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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46C LEU 3.5 12.6 + - - -
47C VAL* 4.2 3.2 - - - +
49C LEU* 6.3 0.2 - - - +
50C ALA* 3.4 27.8 - - - +
108C PHE 3.4 6.7 + - - -
109C SER 3.2 4.7 + - - -
111C GLY* 1.3 74.5 - - - +
113C VAL* 1.3 63.8 + - - +
115C ALA* 3.4 2.6 + - - +
116C VAL* 3.2 23.7 + - - +
266C PHE* 4.0 9.4 - - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 5.4 0.4 - - + -
109C SER 3.1 12.5 + - - +
110C LEU* 3.7 19.5 - - + +
112C GLY* 1.3 76.3 - - - +
114C THR* 1.3 64.5 + - - +
116C VAL* 3.2 4.0 + - - +
117C GLN* 3.0 33.0 + - - +
124C ILE* 3.8 40.2 - - + +
125C PRO 5.2 0.2 - - - +
126C TRP* 4.4 13.5 - - + -
266C PHE* 3.9 12.8 - - + -
270C LEU* 3.7 20.4 - - + -
286C PHE* 4.8 6.5 - - + -
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 3.7 40.3 - - + +
26C ILE* 3.0 36.6 - - + +
27C ALA* 4.1 9.6 - - + +
30C LEU* 4.6 1.6 - - + -
110C LEU* 2.5 42.0 + - - +
111C GLY 3.7 1.6 - - - -
113C VAL* 1.3 72.0 - - - +
115C ALA* 1.3 57.7 + - - +
117C GLN* 3.1 4.2 + - - +
118C GLU* 2.9 31.5 + - + +
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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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26C ILE* 5.2 0.2 - - - +
30C LEU* 4.3 15.5 - - + -
43C GLY* 3.6 31.9 - - - +
46C LEU* 4.1 10.1 - - + -
47C VAL* 4.1 5.8 - - + -
111C GLY 3.0 18.1 + - - +
112C GLY 3.6 4.0 - - - +
114C THR* 1.3 74.7 - - - +
116C VAL* 1.3 68.9 + - - +
118C GLU* 3.3 2.1 + - - +
119C MET* 3.3 29.4 + - - +
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Residues in contact with VAL 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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47C VAL* 3.5 25.6 - - + -
112C GLY 3.2 14.4 + - - +
113C VAL* 3.2 8.0 + - - +
115C ALA* 1.3 78.7 - - - +
117C GLN* 1.3 64.7 + - - +
119C MET* 3.2 11.9 + - - +
120C GLN 3.6 0.2 + - - -
121C GLY* 3.1 22.3 + - - -
122C PRO* 4.2 7.9 - - + +
124C ILE* 3.9 25.4 - - + -
177C LEU* 5.0 0.2 - - + -
198C PHE* 4.0 29.7 - - + +
262C PHE* 4.5 7.9 - - + -
266C PHE* 4.4 11.9 - - + -
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Residues in contact with GLN 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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23C TYR* 3.0 39.2 + - + +
113C VAL* 3.0 24.2 + - + +
114C THR 3.1 4.7 + - - +
116C VAL* 1.3 76.1 - - - +
118C GLU* 1.3 57.6 - - - +
120C GLN* 3.0 21.3 + - - -
121C GLY 3.7 6.6 + - - +
122C PRO 3.9 13.7 - - - +
123C LYS* 3.2 36.2 - - + +
124C ILE* 3.4 13.2 + - + +
286C PHE* 3.2 26.5 + - - +
288C THR* 3.9 15.0 - - + +
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Residues in contact with GLU 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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59A LYS* 6.1 0.3 - - - -
23C TYR* 2.4 27.8 + - + +
27C ALA* 3.8 23.1 - - + +
30C LEU* 4.3 17.7 - - + -
31C ARG* 5.4 2.1 + - - +
114C THR 2.9 20.6 + - - +
115C ALA 3.3 2.9 + - - +
116C VAL 3.3 0.4 - - - -
117C GLN* 1.3 70.9 - - - +
119C MET* 1.3 59.1 + - + +
120C GLN* 3.1 13.9 + - - +
288C THR* 3.2 7.3 - - - -
289C LEU* 3.2 39.6 + - - +
290C GLU 5.1 0.2 + - - -
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Residues in contact with MET 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 6.0 1.3 - - + -
40C ILE 5.4 0.7 - - - +
43C GLY* 3.7 39.0 - - - +
44C PRO* 3.8 11.7 - - - -
47C VAL* 4.2 2.7 - - + -
115C ALA* 3.3 24.7 - - - +
116C VAL* 3.2 3.9 + - - +
117C GLN 3.2 1.2 - - - -
118C GLU* 1.3 79.2 - - + +
120C GLN* 1.4 73.9 + - - +
121C GLY 3.4 2.5 - - - -
177C LEU* 3.8 27.8 - - + -
196C ASN* 3.5 37.0 - - - +
197C VAL* 3.2 1.8 - - - +
198C PHE* 2.6 33.5 + - + +
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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