Contacts of the helix formed by residues 9 - 22 (chain P) in PDB entry 2X86
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 GLY 9 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6P GLY 2.8 14.0 + - - -
8P ALA* 1.3 79.3 - - - +
10P PHE* 1.3 56.7 + - - -
11P ILE 3.7 0.9 - - - -
13P SER* 2.7 35.0 + - - -
31P ASP* 3.2 3.0 + - - -
174P ARG 4.2 0.4 - - - -
177P HIS* 3.8 9.9 - - - -
400P NAP 3.6 25.6 - - - -
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Residues in contact with PHE 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P GLY* 1.3 70.6 - - - -
11P ILE* 1.3 67.4 + - + +
13P SER* 3.0 9.4 + - - -
14P ASN* 2.8 28.1 + - - -
170P VAL* 3.6 32.5 - - + -
171P TYR* 3.5 5.6 - - - -
172P GLY 3.2 33.9 - - - -
173P PRO 3.1 22.4 - - - -
174P ARG 3.1 24.0 - - - +
175P GLU* 3.6 16.8 - - + -
177P HIS* 3.5 1.8 - - + -
178P LYS* 4.0 8.7 - - + -
214P VAL* 3.6 12.3 - - + -
400P NAP 3.0 42.7 + - - +
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Residues in contact with ILE 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P PHE* 1.3 89.2 - - + +
12P GLY* 1.3 62.4 + - - +
14P ASN* 3.1 5.2 + - - +
15P ILE* 3.0 28.7 + - + +
75P GLU* 3.5 21.3 - - - +
167P TYR* 3.5 38.6 - - + +
170P VAL* 4.1 22.0 - - + -
214P VAL* 4.5 8.5 - - + -
217P VAL* 4.0 14.4 - - + -
400P NAP 2.9 41.3 + - + +
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Residues in contact with GLY 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 3.7 16.2 - - - +
6P GLY 3.5 19.0 + - - -
7P GLY* 3.8 7.2 - - - -
10P PHE 3.3 0.4 - - - -
11P ILE* 1.3 80.9 - - - +
13P SER* 1.3 61.1 + - - +
15P ILE* 3.0 6.3 + - - +
16P VAL* 2.9 24.1 + - - +
75P GLU* 4.0 14.6 - - - +
400P NAP 4.4 0.8 + - - -
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Residues in contact with SER 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P GLY 3.3 17.9 + - - -
9P GLY 2.7 25.0 + - - -
10P PHE 3.0 8.5 + - - -
12P GLY* 1.3 74.9 - - - +
14P ASN* 1.3 56.8 + - - +
16P VAL* 3.2 8.0 + - - +
17P LYS* 2.9 24.6 + - - +
41P ASN* 3.6 29.9 - - - +
42P LEU* 4.9 0.2 - - - -
45P LEU* 3.4 7.3 - - - +
174P ARG* 3.3 21.6 - - - +
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Residues in contact with ASN 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P PHE* 2.8 23.0 + - - -
11P ILE 3.1 8.2 + - - +
13P SER* 1.3 79.9 + - - +
15P ILE* 1.3 60.4 + - + +
17P LYS* 3.4 12.8 + - - +
18P ALA* 3.0 28.1 + - - +
173P PRO* 2.9 30.9 + - - +
174P ARG* 3.8 14.7 + - - +
214P VAL* 3.5 36.4 - - + +
215P GLY* 5.3 1.6 + - - -
218P ALA* 3.9 11.8 - - + +
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Residues in contact with ILE 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 4.4 5.6 - - + -
11P ILE* 3.0 20.5 + - + +
12P GLY* 3.0 8.5 + - - +
14P ASN* 1.3 75.6 - - - +
16P VAL* 1.3 65.1 + - - +
18P ALA* 3.2 6.9 + - - +
19P LEU* 2.9 36.6 + - + +
73P PHE* 4.0 27.1 - - + -
75P GLU* 3.6 31.9 - - + +
218P ALA* 4.6 8.7 - - - -
221P ASN* 3.5 38.8 - - + +
222P LEU* 4.4 9.0 - - + -
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Residues in contact with VAL 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P VAL* 4.2 17.0 - - + -
7P GLY 4.2 9.0 - - - +
12P GLY 2.9 18.3 + - - +
13P SER 3.3 7.6 - - - +
15P ILE* 1.3 77.3 - - - +
17P LYS* 1.3 58.3 + - - +
19P LEU* 3.1 11.7 + - - +
20P ASN* 2.8 30.2 + - - +
27P ILE* 4.0 11.0 - - + -
29P VAL* 4.1 22.2 - - + -
42P LEU* 4.7 1.1 - - + -
45P LEU* 3.7 21.8 - - + -
47P ILE* 3.8 25.1 - - + -
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Residues in contact with LYS 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P SER 2.9 13.3 + - - +
14P ASN* 3.7 15.0 - - - +
15P ILE 3.3 0.2 - - - -
16P VAL* 1.3 74.6 - - - +
18P ALA* 1.3 58.0 + - - +
20P ASN* 3.1 6.6 + - + +
21P ASP* 2.8 60.8 + - - +
45P LEU* 3.9 27.8 - - + +
174P ARG* 4.0 20.8 - - - +
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Residues in contact with ALA 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASN 3.0 17.7 + - - +
15P ILE* 3.5 5.8 - - - +
16P VAL 3.2 0.2 - - - -
17P LYS* 1.3 78.6 - - - +
19P LEU* 1.3 60.4 + - - +
21P ASP* 3.2 12.3 + - - +
22P LYS* 3.1 18.7 + - - +
218P ALA* 4.0 20.2 - - + +
219P ASP* 5.3 4.3 - - - +
222P LEU* 3.8 26.9 - - + +
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Residues in contact with LEU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P ILE* 3.9 45.3 - - + -
4P VAL* 4.2 6.7 - - + -
15P ILE* 2.9 32.6 + - + +
16P VAL 3.4 6.1 - - - +
18P ALA* 1.3 71.8 - - - +
20P ASN* 1.3 67.8 + - - +
22P LYS* 3.0 11.2 + - + +
23P GLY 3.3 0.2 + - - -
24P ILE* 2.9 39.2 + - + +
27P ILE* 3.9 23.1 - - + -
73P PHE* 4.4 3.6 - - + -
222P LEU* 3.9 26.0 - - + -
225P LEU* 5.1 3.6 - - + -
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Residues in contact with ASN 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P VAL* 2.8 17.1 + - - -
17P LYS* 3.3 12.3 - - + +
19P LEU* 1.3 76.4 - - - +
21P ASP* 1.3 56.6 + - - +
23P GLY* 2.7 26.5 + - - -
24P ILE 2.9 19.4 + - - -
25P THR* 3.8 8.5 - - + +
27P ILE* 3.8 4.4 - - - +
44P ASP 5.0 0.2 - - - +
45P LEU* 3.5 15.4 - - + +
46P ASN* 2.8 55.4 + - - +
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Residues in contact with ASP 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H GLU* 5.6 1.0 - - - +
17P LYS* 2.8 51.7 + - - +
18P ALA* 3.2 13.0 + - - +
20P ASN* 1.3 78.6 - - - +
22P LYS* 1.3 60.2 + - + +
23P GLY 3.2 1.4 + - - -
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Residues in contact with LYS 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ASP* 6.2 0.2 - - - +
128H ILE* 3.4 10.3 - - - +
132H GLU* 5.3 13.3 + - - +
133H TYR* 2.6 41.8 + - + +
18P ALA 3.1 12.6 + - - +
19P LEU* 3.0 10.9 + - + +
21P ASP* 1.3 78.2 - - + +
23P GLY* 1.3 60.6 + - - +
24P ILE* 3.3 10.8 + - + +
222P LEU* 3.8 23.8 - - + -
226P GLU* 3.1 30.7 + - - +
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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