Contacts of the helix formed by residues 9 - 22 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B GLY 2.7 14.7 + - - -
8B ALA* 1.3 80.5 - - - +
10B PHE* 1.3 56.6 - - - -
11B ILE 3.7 0.9 - - - -
13B SER* 2.7 35.0 + - - -
31B ASP* 3.2 4.9 + - - -
38B LYS* 4.9 0.2 - - - -
41B ASN* 4.2 0.7 - - - -
177B HIS* 3.9 9.4 - - - -
400B NAP 3.6 23.1 - - - -
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 1.3 70.2 - - - -
11B ILE* 1.3 68.2 + - + +
13B SER* 3.0 9.7 + - - -
14B ASN* 2.8 27.8 + - - -
170B VAL* 3.6 32.3 - - + -
171B TYR* 3.6 5.8 - - - -
172B GLY 3.2 33.7 - - - -
173B PRO 3.1 21.8 - - - -
174B ARG 3.1 25.6 - - - +
175B GLU* 3.6 15.9 - - + -
177B HIS* 3.5 2.7 - - + -
178B LYS* 4.0 10.3 - - + -
214B VAL* 3.6 13.0 - - + -
400B NAP 3.1 42.2 + - - +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 1.3 88.8 - - + +
12B GLY* 1.3 64.8 + - - +
14B ASN* 3.1 9.4 + - + +
15B ILE* 3.0 27.9 + - + +
75B GLU* 3.5 22.2 - - - +
167B TYR* 3.5 38.4 - - + +
170B VAL* 4.1 21.3 - - + -
214B VAL* 4.5 5.6 - - + -
217B VAL* 4.0 14.4 - - + -
400B NAP 2.8 42.2 + - + +
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Residues in contact with GLY 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.7 15.6 - - - +
6B GLY 3.5 19.5 + - - -
7B GLY* 3.8 5.8 - - - -
9B GLY 4.3 0.2 - - - -
10B PHE 3.3 0.6 - - - -
11B ILE* 1.3 79.1 - - - +
13B SER* 1.3 63.0 + - - +
15B ILE* 3.0 6.6 + - - +
16B VAL* 2.9 23.6 + - - +
75B GLU* 4.0 15.0 - - - +
400B NAP 4.3 1.0 + - - -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLY 3.3 17.7 + - - -
9B GLY 2.7 24.7 + - - -
10B PHE 3.0 8.5 + - - -
12B GLY* 1.3 75.1 - - - +
14B ASN* 1.3 56.6 + - - +
16B VAL* 3.2 8.0 + - - +
17B LYS* 2.9 24.3 + - - +
41B ASN* 3.6 30.4 - - - +
45B LEU* 3.4 7.8 - - - +
174B ARG* 3.3 21.8 - - - +
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 2.8 22.6 + - - -
11B ILE 3.1 8.8 + - - +
13B SER* 1.3 80.1 + - - +
15B ILE* 1.3 59.0 + - - +
17B LYS* 3.4 12.0 + - - +
18B ALA* 3.0 28.4 + - - +
173B PRO* 2.9 30.2 + - - +
174B ARG* 3.8 14.3 + - - +
214B VAL* 3.5 37.1 - - + +
215B GLY* 5.3 1.4 + - - -
218B ALA* 3.9 12.0 - - + +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 4.4 6.3 - - + -
11B ILE* 3.0 20.7 + - + +
12B GLY* 3.0 7.8 + - - +
14B ASN* 1.3 74.8 - - - +
16B VAL* 1.3 65.0 + - - +
18B ALA* 3.2 6.3 + - - +
19B LEU* 2.9 37.1 + - + +
73B PHE* 4.0 28.0 - - + -
75B GLU* 3.6 31.6 - - + +
218B ALA* 4.7 8.7 - - + -
221B ASN* 3.5 38.8 - - + +
222B LEU* 4.5 6.1 - - + -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 4.2 17.3 - - + -
7B GLY 4.2 8.5 - - - +
12B GLY 2.9 19.3 + - - +
13B SER 3.3 7.9 - - - +
15B ILE* 1.3 76.0 - - - +
17B LYS* 1.3 57.2 + - - +
19B LEU* 3.1 11.1 + - - +
20B ASN* 2.8 30.2 + - - +
27B ILE* 4.0 10.5 - - + -
29B VAL* 4.1 22.0 - - + -
42B LEU* 4.7 1.8 - - + -
45B LEU* 3.7 21.5 - - + -
47B ILE* 3.8 25.6 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER 2.9 14.8 + - - +
14B ASN* 3.7 15.5 - - - +
15B ILE 3.3 0.4 - - - -
16B VAL* 1.3 75.0 - - - +
18B ALA* 1.3 58.2 + - - +
20B ASN* 3.1 7.5 + - + +
21B ASP* 2.9 60.4 + - - +
45B LEU* 3.9 27.8 - - + +
174B ARG* 4.1 19.5 - - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN 3.0 17.7 + - - +
15B ILE* 3.5 5.8 - - - +
17B LYS* 1.3 77.9 - - - +
19B LEU* 1.3 60.1 - - - +
21B ASP* 3.2 12.5 + - - +
22B LYS* 3.1 18.5 + - - +
218B ALA* 4.0 19.7 - - + +
219B ASP* 5.3 4.5 - - - +
222B LEU* 3.8 26.7 - - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.8 45.8 - - + -
4B VAL* 4.2 7.9 - - + -
15B ILE* 2.9 31.7 + - + +
16B VAL 3.4 6.3 - - - +
18B ALA* 1.3 72.7 - - - +
20B ASN* 1.3 66.8 + - - +
22B LYS* 3.0 10.4 + - + +
23B GLY 3.3 0.2 + - - -
24B ILE* 2.9 40.4 + - + +
27B ILE* 3.9 22.2 - - + -
73B PHE* 4.4 4.0 - - + -
222B LEU* 3.9 26.5 - - + -
225B LEU* 5.0 3.6 - - + -
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 2.8 17.3 + - - -
17B LYS* 3.3 11.7 - - + +
19B LEU* 1.3 75.6 - - - +
21B ASP* 1.3 57.3 + - - +
23B GLY* 2.7 26.7 + - - -
24B ILE 2.9 19.2 + - - -
25B THR* 3.8 8.2 - - + +
27B ILE* 3.8 4.0 - - - +
45B LEU* 3.6 16.1 - - + +
46B ASN* 2.8 55.0 + - - +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 2.9 51.2 + - - +
18B ALA* 3.2 12.6 + - - +
20B ASN* 1.3 77.9 - - - +
22B LYS* 1.3 60.2 + - + +
23B GLY 3.2 0.7 + - - -
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA 3.1 10.3 + - - +
19B LEU* 3.0 11.8 + - + +
21B ASP* 1.3 77.3 - - + +
23B GLY* 1.3 61.4 + - - +
24B ILE* 3.3 16.7 + - + +
222B LEU* 3.8 23.6 - - + -
226B GLU* 3.1 30.8 + - - +
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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