Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 2Y4W
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 THR 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 85.5 + - - +
4A PRO* 1.3 76.5 - - - +
5A ALA* 3.3 12.3 - - + +
6A ARG* 3.2 38.8 + - + +
7A ARG* 3.7 12.5 + - - +
61A GLU* 3.6 34.2 + - + +
62A GLU 4.9 0.5 + - - -
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Residues in contact with PRO 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 THR* 1.3 93.5 - - - +
5A ALA* 1.3 67.9 + - + +
6A ARG 3.1 2.5 - - - -
7A ARG* 3.3 11.0 + - + +
8A ARG* 3.2 31.5 + - + +
61A GLU 5.5 0.4 - - - +
62A GLU 5.6 3.4 - - - +
63A TYR* 6.3 2.9 - - + -
64A PRO* 4.5 11.2 - - + -
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Residues in contact with ALA 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 THR* 3.3 9.8 - - + +
4A PRO* 1.3 81.8 - - + +
6A ARG* 1.3 62.0 + - - +
8A ARG* 3.6 3.3 + - - +
9A LEU* 3.3 29.0 + - + +
60A SER 4.1 17.3 - - - +
61A GLU* 4.3 4.7 - - - +
62A GLU 4.7 0.7 - - - +
63A TYR* 4.0 10.1 - - - -
64A PRO* 3.8 36.1 - - + +
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Residues in contact with ARG 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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1A MET 3.6 22.2 + - - -
2A SER* 5.2 3.7 - - - +
3A THR* 3.2 28.1 - - + +
4A PRO 3.1 0.4 - - - -
5A ALA* 1.3 75.6 - - - +
7A ARG* 1.3 66.4 + - - +
9A LEU* 3.2 21.5 + - - +
10A MET* 3.3 34.7 + - + +
33A ILE* 3.6 31.0 - - + +
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Residues in contact with ARG 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 SER* 5.5 4.8 + - - -
3A THR 3.7 11.0 + - - +
4A PRO* 3.3 12.9 + - + +
6A ARG* 1.3 78.7 - - - +
8A ARG* 1.3 64.5 + - + +
10A MET* 3.0 28.1 + - + +
11A ARG* 3.2 47.6 + - + +
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Residues in contact with ARG 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 PRO* 3.2 18.0 + - - +
5A ALA 3.7 7.4 - - - +
6A ARG 3.2 0.2 - - - -
7A ARG* 1.3 78.2 - - - +
9A LEU* 1.3 63.7 + - + +
11A ARG* 2.9 55.3 + - - +
12A ASP* 3.0 13.4 + - - +
64A PRO* 4.1 26.4 - - + +
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Residues in contact with LEU 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 ALA* 3.3 16.8 + - + +
6A ARG* 3.2 12.4 + - + +
8A ARG* 1.3 78.5 - - + +
10A MET* 1.3 60.4 + - - +
12A ASP* 3.5 9.4 + - + +
13A PHE* 3.2 22.2 + - - +
33A ILE* 3.7 32.5 - - + +
34A MET* 6.1 0.4 - - - -
36A TRP* 4.0 16.4 - - + -
59A PHE* 3.6 52.9 - - + -
60A SER 5.5 4.3 - - - +
102A VAL* 6.5 0.4 - - + -
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Residues in contact with MET 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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6A ARG* 3.5 48.7 - - + +
7A ARG* 3.0 18.7 + - + +
9A LEU* 1.3 78.6 - - - +
11A ARG* 1.3 62.6 + - + +
12A ASP 3.5 0.2 + - - -
13A PHE* 3.6 13.7 + - - +
14A LYS* 3.6 14.4 + - - +
33A ILE* 3.9 13.9 - - + -
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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 ARG* 3.3 50.4 - - + +
8A ARG* 2.9 49.1 + - - +
10A MET* 1.3 76.9 - - + +
12A ASP* 1.3 61.2 + - - +
14A LYS* 3.1 38.9 - - - +
15A ARG* 3.4 8.1 + - - +
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Residues in contact with ASP 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 ARG 3.0 11.3 + - - +
9A LEU* 3.7 13.9 - - + +
11A ARG* 1.3 77.7 - - - +
13A PHE* 1.3 60.4 + - - +
15A ARG* 3.2 7.0 + - - +
16A LEU* 2.8 28.7 + - - +
36A TRP* 3.7 11.4 - - + -
101A ASP* 3.3 37.7 - - - +
102A VAL* 3.0 33.2 + - - +
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Residues in contact with PHE 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 LEU 3.2 14.2 + - - +
10A MET* 3.8 9.0 - - - +
12A ASP* 1.3 82.1 + - - +
14A LYS* 1.3 66.3 + - + +
16A LEU* 2.9 23.6 + - + +
17A GLN* 3.2 32.5 + - + +
27A ALA* 3.9 16.6 - - + -
28A PRO* 3.7 41.3 - - + -
36A TRP* 4.5 9.4 - + + -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A MET 3.6 11.5 + - - +
11A ARG* 3.1 31.2 - - - +
13A PHE* 1.3 81.7 - - + +
15A ARG* 1.3 112.4 + - - +
17A GLN* 3.2 19.7 + - - +
18A GLU* 3.3 21.1 + - + +
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Residues in contact with ARG 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 3.4 13.0 + - - +
12A ASP* 3.2 8.7 + - - +
13A PHE 3.2 0.4 - - - -
14A LYS* 1.3 111.5 - - - +
16A LEU* 1.3 60.2 + - - +
18A GLU* 3.5 21.2 + - - +
19A ASP* 3.5 12.8 + - - +
101A ASP* 5.1 12.6 - - - +
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Residues in contact with LEU 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 ASP* 2.8 14.6 + - - +
13A PHE* 2.9 16.6 + - + +
15A ARG* 1.3 76.9 - - - +
17A GLN* 1.3 63.6 + - - +
19A ASP 4.7 1.3 - - - +
20A PRO* 2.9 44.0 - - + +
21A PRO* 3.6 31.0 - - + -
26A GLY 3.0 34.1 - - - +
27A ALA* 3.6 20.2 - - + -
36A TRP* 5.0 3.1 - - + -
102A VAL* 4.4 16.8 - - + -
103A SER* 5.0 4.5 - - - +
106A LEU* 5.6 0.7 - - + -
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Residues in contact with GLN 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 PHE* 3.6 39.6 - - + +
14A LYS* 3.2 12.2 + - - +
16A LEU* 1.3 85.7 - - - +
18A GLU* 1.3 69.8 + - - +
19A ASP 3.4 0.2 + - - -
20A PRO* 3.9 9.3 - - - +
27A ALA* 4.9 2.9 - - - +
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Residues in contact with GLU 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 LYS* 3.3 19.6 + - + +
15A ARG* 3.6 20.9 - - - +
16A LEU 3.3 0.6 - - - -
17A GLN* 1.3 83.6 - - - +
19A ASP* 1.3 63.7 + - + +
20A PRO* 4.5 0.3 - - - +
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Residues in contact with ASP 19 (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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15A ARG 3.5 8.4 + - - +
16A LEU* 3.4 4.8 + - - +
18A GLU* 1.3 85.8 - - + +
20A PRO* 1.3 71.1 - - - +
21A PRO* 4.0 1.6 - - - +
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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