Contacts of the helix formed by residues 3 - 18 (chain A) in PDB entry 2PEG
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SER* 3.6 2.7 + - - -
2A LEU* 1.3 74.1 - - - +
4A ASP* 1.3 66.6 + - - +
5A LYS* 3.4 11.8 + - - +
6A ASP* 3.0 32.3 + - - -
7A LYS* 2.9 21.4 + - - +
128A LYS* 5.0 2.0 + - - -
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Residues in contact with ASP 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 1.3 74.5 - - - +
5A LYS* 1.3 56.6 + - - +
7A LYS* 3.7 20.1 + - - +
8A ALA* 3.0 31.0 + - - +
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Residues in contact with LYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 3.0 10.0 + - - +
4A ASP* 1.3 80.0 - - - +
6A ASP* 1.3 61.3 + - - +
8A ALA* 3.4 5.7 + - - +
9A ALA* 3.0 28.2 + - + +
121A GLU* 6.4 1.8 - - - -
125A SER* 5.3 4.5 - - - +
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Residues in contact with ASP 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.6 17.2 - - + -
3A SER* 3.0 31.3 + - - +
5A LYS* 1.3 79.4 - - - +
7A LYS* 1.3 66.7 + - - +
9A ALA* 3.3 1.4 + - - +
10A VAL* 3.0 31.1 + - - +
74A ILE* 5.3 0.2 - - - -
124A VAL* 5.1 1.6 - - - +
125A SER* 2.7 34.5 + - - +
128A LYS* 2.8 41.6 + - - +
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.7 28.4 + - + -
3A SER 2.9 17.2 + - - +
4A ASP* 3.7 18.2 + - - +
6A ASP* 1.3 76.2 - - - +
8A ALA* 1.3 63.1 + - - +
10A VAL* 3.4 1.6 + - - +
11A ARG* 3.0 45.8 + - - +
74A ILE* 4.0 38.0 - - + +
75A ASP* 2.8 38.4 + - - +
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASP 3.0 18.3 + - - +
5A LYS* 3.7 6.3 - - - +
7A LYS* 1.3 77.6 - - - +
9A ALA* 1.3 55.9 + - - +
11A ARG* 3.3 9.5 + - - +
12A ALA* 2.9 31.6 + - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.0 19.6 + - + +
6A ASP 3.3 0.2 + - - -
8A ALA* 1.3 75.4 - - - +
10A VAL* 1.3 58.4 + - - +
12A ALA* 3.4 5.6 + - - +
13A LEU* 2.9 31.0 + - - +
121A GLU 4.9 6.7 - - - +
122A ALA* 5.2 8.3 - - - +
125A SER* 3.7 25.8 - - - +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 5.7 0.4 - - + -
6A ASP* 3.0 23.4 + - + +
9A ALA* 1.3 76.0 - - - +
11A ARG* 1.3 63.3 + - - +
13A LEU* 3.3 5.2 + - - +
14A TRP* 2.9 23.4 + - + +
71A VAL* 4.1 19.7 - - + -
74A ILE* 3.8 23.6 - - + -
125A SER* 3.7 28.7 - - - +
126A LEU* 4.1 17.7 - - + +
129A PHE* 3.7 26.2 - - + -
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.0 45.6 + - - +
8A ALA* 3.8 7.5 - - - +
10A VAL* 1.3 76.0 - - - +
12A ALA* 1.3 56.2 + - - +
14A TRP* 3.5 1.4 + - - +
15A SER* 2.9 28.9 + - - -
71A VAL* 4.2 26.9 + - + +
72A SER* 5.0 5.1 + - - +
74A ILE* 3.4 19.2 - - + +
75A ASP* 3.1 26.9 + - - -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA 2.9 17.2 + - - +
9A ALA* 3.8 6.3 - - - +
11A ARG* 1.3 73.9 - - - +
13A LEU* 1.3 66.5 + - - +
15A SER* 3.3 8.2 - - - -
16A LYS* 3.2 39.7 + - - +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 2.9 18.2 + - - +
10A VAL* 3.8 3.8 - - - +
12A ALA* 1.3 75.0 - - - +
14A TRP* 1.3 58.8 + - + +
16A LYS* 2.9 13.8 + - + +
17A ILE* 2.8 53.5 + - + +
110A ILE* 4.9 1.6 - - + -
117A GLU* 3.9 32.3 - - + +
118A PHE* 4.3 15.3 - - + +
122A ALA* 4.3 15.7 - - + +
126A LEU* 3.8 41.5 - - + -
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Residues in contact with TRP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 2.9 18.1 + - + +
11A ARG 3.9 3.4 - - - +
13A LEU* 1.3 75.0 - - + +
15A SER* 1.3 62.3 + - - +
17A ILE* 3.7 28.3 - - + -
18A GLY* 2.7 44.8 + - - -
21A ALA* 3.7 32.1 - - + -
24A ILE* 4.7 2.7 - - + -
64A MET* 3.8 31.9 - - + -
67A ILE* 4.4 7.9 - - + -
68A ALA* 3.8 35.0 - - + +
71A VAL* 3.9 35.2 - - + -
110A ILE* 5.6 1.3 - - + -
126A LEU* 6.2 4.0 - - + -
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG 2.9 19.1 + - - -
12A ALA* 3.3 11.0 - - - -
13A LEU 3.2 0.2 - - - -
14A TRP* 1.3 78.2 - - - +
16A LYS* 1.3 62.4 + - - +
18A GLY* 4.4 1.9 + - - -
19A LYS* 5.3 2.1 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.3 26.8 - - - +
13A LEU* 2.9 11.3 + - + +
15A SER* 1.3 82.2 - - - +
17A ILE* 1.3 61.0 + - + +
19A LYS* 3.6 22.9 - - - +
114A PHE* 4.4 2.5 - - - -
117A GLU* 3.9 36.3 + - + +
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 2.8 50.0 + - + +
14A TRP* 3.7 25.6 - - + -
16A LYS* 1.3 76.9 - - + +
18A GLY* 1.4 58.0 + - - +
19A LYS* 3.1 3.4 - - - -
20A SER* 2.8 33.5 + - - -
21A ALA 3.8 2.3 + - - -
24A ILE* 4.1 7.0 - - + +
110A ILE* 3.7 37.5 - - + -
114A PHE* 3.5 44.9 - - + -
117A GLU* 4.7 1.6 - - + -
126A LEU* 6.4 0.2 - - + -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 2.7 50.5 + - - -
15A SER 4.4 1.3 + - - -
16A LYS 3.6 1.0 - - - -
17A ILE* 1.4 71.9 - - - +
19A LYS* 1.3 61.4 + - - +
21A ALA* 3.1 20.4 + - - +
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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
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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