Contacts of the helix formed by residues 14 - 24 (chain A) in PDB entry 2A4X
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 ASP 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.0 3.9 - - - +
13A GLU* 1.3 89.7 - - + +
15A MET* 1.3 63.8 + - - +
16A ALA* 3.1 13.2 + - - +
17A LYS* 2.8 59.9 + - + +
18A SER* 3.1 23.4 + - - -
119A ASP* 4.6 2.1 + - - +
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Residues in contact with MET 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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12A VAL* 4.0 10.7 - - + +
13A GLU 4.3 0.4 + - - -
14A ASP* 1.3 73.2 + - - +
16A ALA* 1.3 64.6 + - - +
18A SER* 3.2 2.1 + - - -
19A LEU* 2.9 41.4 + - + +
33A ALA 3.5 21.8 - - - +
34A ASP 4.0 7.2 - - - +
36A ALA 3.3 23.1 - - - +
37A PRO 3.6 16.4 - - - +
38A HIS 3.8 1.8 - - - +
39A THR* 3.5 16.2 - - - +
51A TRP* 3.5 45.8 - - + +
53A THR* 3.9 17.1 - - + +
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Residues in contact with ALA 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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14A ASP* 3.1 8.5 + - - +
15A MET* 1.3 79.2 - - - +
17A LYS* 1.3 64.1 + - + +
19A LEU* 3.8 1.4 - - - +
20A GLU* 3.0 25.6 + - - +
23A ARG* 4.5 0.7 + - - -
34A ASP* 3.7 42.3 + - + +
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Residues in contact with LYS 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 GLU* 4.5 12.4 + - - +
14A ASP* 2.8 42.8 + - + +
16A ALA* 1.3 75.1 - - + +
18A SER* 1.3 63.7 + - - +
20A GLU* 3.5 5.2 + - - +
21A PHE* 3.4 10.0 + - - +
97A TYR* 4.5 2.8 + - - -
118A PRO* 3.4 26.7 - - + +
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Residues in contact with SER 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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10A VAL* 5.0 0.2 - - - +
12A VAL* 3.3 22.2 - - - +
14A ASP 3.1 17.3 + - - -
15A MET* 3.8 2.7 - - - -
17A LYS* 1.3 75.6 - - - +
19A LEU* 1.3 64.3 + - - +
21A PHE* 3.1 11.6 + - - +
22A TYR* 3.1 28.3 + - - -
51A TRP* 3.3 25.4 + - - -
117A ASP* 4.9 1.7 + - - -
118A PRO* 3.9 12.9 - - - +
119A ASP* 4.0 8.5 + - - -
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Residues in contact with LEU 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 MET* 2.9 32.2 + - + +
16A ALA 3.8 3.6 - - - +
18A SER* 1.3 77.8 - - - +
20A GLU* 1.3 61.4 - - - +
22A TYR* 3.3 3.0 + - - +
23A ARG* 2.9 43.0 + - - +
29A ILE* 3.9 16.6 - - + +
33A ALA* 3.5 39.0 - - + +
34A ASP* 3.5 16.4 - - - +
39A THR* 4.1 1.3 - - + +
51A TRP* 3.6 43.1 - - + -
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Residues in contact with GLU 20 (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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16A ALA 3.0 16.7 + - - +
17A LYS* 4.0 6.1 - - - +
18A SER 3.3 0.4 - - - -
19A LEU* 1.3 76.7 - - - +
21A PHE* 1.3 63.0 + - - +
23A ARG* 2.7 42.3 + - - +
24A LYS* 3.1 48.9 + - - +
97A TYR* 4.1 6.7 - - - +
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Residues in contact with PHE 21 (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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17A LYS 3.4 2.6 + - - -
18A SER 3.1 8.8 + - - +
20A GLU* 1.3 77.4 - - - +
22A TYR* 1.3 85.2 + + - +
24A LYS* 3.0 25.8 + - - +
25A LEU* 3.4 33.3 + - + +
92A LEU* 4.3 15.3 - - + -
97A TYR* 3.7 43.6 + + + +
115A VAL* 4.0 14.6 - - + -
116A LYS 3.6 16.6 - - - -
117A ASP* 3.5 21.8 - - + -
118A PRO* 3.4 22.7 - - + -
123A VAL* 4.0 7.9 - - + -
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Residues in contact with TYR 22 (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* 5.2 5.1 - - + +
18A SER* 3.1 36.0 + - - +
19A LEU 3.3 4.5 + - - +
21A PHE* 1.3 96.7 - + - +
23A ARG* 1.3 65.5 + - - +
25A LEU* 3.0 11.5 + - - +
27A VAL* 3.1 29.9 + - + +
29A ILE* 4.1 4.9 - - + -
49A LEU* 4.6 6.3 - - + -
51A TRP* 3.5 37.2 - + + -
75A ILE* 3.8 25.9 - - + +
77A PHE* 3.8 33.4 - + - -
117A ASP* 2.7 30.7 + - + +
118A PRO* 5.0 0.2 - - + -
121A ASN* 4.8 1.6 + - - +
123A VAL* 3.9 6.1 - - + +
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Residues in contact with ARG 23 (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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16A ALA 4.5 0.4 + - - -
19A LEU* 2.9 28.7 + - - +
20A GLU* 2.7 59.8 + - - +
21A PHE 3.2 0.2 - - - -
22A TYR* 1.3 77.3 - - - +
24A LYS* 1.3 61.1 + - - +
25A LEU 3.1 0.2 - - - -
26A GLY* 3.2 14.6 + - - -
27A VAL 3.6 19.1 + - - +
29A ILE* 2.9 30.3 + - + +
30A PRO 2.9 24.4 + - - -
31A ALA* 3.5 11.9 - - - +
34A ASP* 2.7 35.5 + - - -
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Residues in contact with LYS 24 (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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20A GLU* 3.1 43.4 + - - +
21A PHE 3.0 13.6 + - - +
23A ARG* 1.3 77.5 - - - +
25A LEU* 1.3 53.3 + - - +
26A GLY 3.4 1.5 + - - -
88A LYS* 2.7 34.7 + - - +
91A GLU* 3.7 21.8 - - + +
92A LEU* 3.8 15.0 - - + -
95A ALA* 4.4 16.0 - - + +
97A TYR* 3.8 24.8 + - + -
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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