Contacts of the helix formed by residues 1 - 14 (chain A) in PDB entry 1AYP
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 ASN 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 1.3 60.5 + - - +
3A VAL* 2.6 46.5 + - - +
4A ASN* 3.1 28.2 + - - +
5A PHE* 3.0 25.0 + - - +
51A TYR* 4.6 1.4 + - - -
61A THR 3.5 11.1 + - - -
62A LYS 3.2 14.1 - - - -
63A PHE* 3.2 16.6 + - - +
64A LEU 2.8 27.6 + - - +
65A SER* 3.4 16.6 + - - -
66A TYR* 3.5 17.4 - - - -
87A LEU* 3.9 1.4 - - - +
91A ASP* 3.9 4.5 + - - +
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Residues in contact with LEU 2 (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 ASN* 1.3 72.7 + - - +
3A VAL* 1.3 61.2 + - + +
5A PHE* 3.6 14.3 - - + +
6A HIS* 2.8 28.2 + - - +
51A TYR* 4.9 4.5 - - - +
62A LYS* 2.9 47.3 + - + +
63A PHE* 5.1 11.0 - - + -
201A INB 3.5 74.9 - - + +
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN* 2.6 23.1 + - - +
2A LEU* 1.3 73.3 - - + +
4A ASN* 1.3 57.7 + - - +
6A HIS* 2.8 29.6 + - + +
7A ARG* 2.9 41.9 + - + +
201A INB 5.7 4.7 - - + -
111B TYR* 4.0 33.4 - - + -
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Residues in contact with ASN 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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1A ASN* 3.1 31.9 + - - +
3A VAL* 1.3 80.2 - - - +
5A PHE* 1.3 56.4 + - - +
7A ARG* 3.5 5.5 + - - +
8A MET* 3.0 27.9 + - - +
65A SER* 3.7 1.7 - - - +
66A TYR* 3.1 68.2 + - + +
68A PHE* 3.8 17.5 - - + -
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Residues in contact with PHE 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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1A ASN 3.0 8.0 + - - +
2A LEU* 3.6 21.1 - - + +
4A ASN* 1.3 74.4 - - - +
6A HIS* 1.3 68.1 + - - +
8A MET* 3.1 5.4 + - + +
9A ILE* 3.0 47.6 + - + +
47A HIS* 3.2 34.1 - + - -
51A TYR* 4.8 1.3 - - - +
66A TYR* 3.4 3.0 + - - -
91A ASP* 3.3 49.8 - - + +
94A ALA* 3.8 16.2 - - + -
95A ALA* 4.3 2.5 - - + -
98A PHE* 4.2 7.4 - + - -
201A INB 3.6 35.2 - - + -
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Residues in contact with HIS 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 2.8 14.7 + - - +
3A VAL* 2.8 22.9 + - + +
5A PHE* 1.3 71.9 - - - +
7A ARG* 1.4 64.4 + - - +
9A ILE* 3.3 4.0 + - - +
10A LYS* 3.1 26.9 + - + +
16A GLU* 4.3 19.5 - - + +
17A ALA* 3.6 37.4 + - + +
18A ALA* 3.9 11.6 + - + +
201A INB 3.6 27.1 - - + +
111B TYR* 6.0 4.6 - + - -
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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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3A VAL* 2.9 31.1 + - + +
4A ASN* 4.2 6.2 - - - +
6A HIS* 1.4 72.4 + - - +
8A MET* 1.3 69.2 + - - +
10A LYS* 3.7 8.9 - - + +
11A LEU* 3.1 30.3 + - + +
68A PHE* 4.7 9.6 - - + -
107B LYS* 3.0 42.4 + - - +
108B LYS* 4.3 8.2 + - - +
110B GLN* 3.9 6.9 + - - -
111B TYR* 3.4 39.6 - - - +
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Residues in contact with MET 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 ASN 3.0 13.7 + - - +
5A PHE* 3.1 13.7 + - + +
7A ARG* 1.3 76.8 - - - +
9A ILE* 1.3 60.6 + - - +
11A LEU* 3.5 16.0 + - - +
12A THR* 3.4 16.1 + - - +
66A TYR* 3.5 19.7 - - + -
68A PHE* 4.0 12.9 - - + -
75A ILE* 3.3 41.0 - - + +
77A CYS* 4.2 1.3 - - - -
88A CYS* 3.8 27.1 - - - +
91A ASP* 3.8 3.8 - - - -
92A LYS* 3.4 38.4 - - + +
95A ALA* 3.9 16.4 - - + +
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Residues in contact with ILE 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 PHE* 3.0 42.1 + - + +
6A HIS 3.6 5.6 - - - +
7A ARG 3.2 0.2 - - - -
8A MET* 1.3 73.4 - - - +
10A LYS* 1.3 64.5 + - - +
12A THR* 3.2 6.8 + - - -
13A THR* 2.7 52.2 + - + +
15A LYS 4.7 2.2 - - - +
17A ALA* 3.6 29.2 - - + -
21A TYR* 4.1 16.4 - - + -
95A ALA* 4.1 4.0 - - + -
98A PHE* 3.6 29.2 - - + -
201A INB 4.2 9.4 - - + -
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Residues in contact with LYS 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 HIS* 3.1 20.8 + - + +
7A ARG* 3.3 12.1 + - - +
9A ILE* 1.3 73.5 - - - +
11A LEU* 1.3 57.5 + - + +
14A GLY* 2.7 56.5 + - - +
15A LYS 3.2 23.3 + - - +
16A GLU* 3.0 32.6 + - - +
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Residues in contact with LEU 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* 3.1 19.1 + - + +
8A MET 3.6 4.5 - - - +
10A LYS* 1.3 77.4 - - + +
12A THR* 1.3 56.6 + - - +
14A GLY* 4.4 1.4 + - - -
68A PHE* 4.2 15.3 - - + -
70A ASN* 3.6 36.8 - - + +
72A GLY 4.0 5.2 - - - +
73A SER* 2.8 26.8 + - - -
75A ILE* 3.5 30.5 - - + -
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Residues in contact with THR 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 MET 3.4 13.1 + - - +
9A ILE* 3.2 7.8 + - - -
11A LEU* 1.3 77.8 - - - +
13A THR* 1.3 63.5 + - - +
73A SER* 3.6 30.8 + - - +
75A ILE* 4.3 11.9 - - + -
95A ALA* 3.1 39.1 + - + +
96A THR* 4.6 7.9 - - - +
99A ALA* 3.6 21.0 - - + +
102A LYS* 4.8 3.6 - - - +
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Residues in contact with THR 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 ILE* 2.7 33.8 + - + +
12A THR* 1.3 90.6 - - - +
14A GLY* 1.4 57.7 + - - +
15A LYS* 3.0 26.7 + - - +
21A TYR* 4.4 4.3 - - - +
95A ALA 3.9 0.2 - - - +
98A PHE* 3.7 19.5 - - + -
99A ALA* 3.5 27.6 - - - +
102A LYS* 3.3 35.2 + - + +
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Residues in contact with GLY 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 LYS* 2.7 51.6 + - - -
11A LEU 4.4 1.6 + - - -
12A THR 3.7 0.6 - - - -
13A THR* 1.4 69.0 + - - +
15A LYS* 1.3 58.1 + - - +
16A GLU* 4.4 0.5 - - - +
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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
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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