Contacts of the strand formed by residues 24 - 30 (chain B) in PDB entry 2IGT
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 PHE 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B SER* 5.8 2.5 - - - -
20B GLY* 2.6 49.4 - - - +
22B GLY* 2.8 5.5 + - - -
23B ASP* 1.3 81.6 - - - +
25B HIS* 1.3 62.6 + - - +
26B LEU* 3.8 24.2 - - + -
36B GLU* 3.7 15.7 - - + -
37B GLN 3.2 14.8 - - - -
38B TYR* 3.4 41.5 - + + -
95B LEU* 4.5 10.6 - - + +
114B PRO* 3.5 37.9 - - + -
115B GLU* 5.2 0.7 - - - -
284B ILE* 4.0 31.9 - - + -
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Residues in contact with HIS 25 (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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19B SER 3.7 17.7 - - - +
20B GLY* 3.8 8.6 + - - +
22B GLY 4.8 4.0 + - - -
23B ASP 5.7 0.2 - - - -
24B PHE* 1.3 92.0 + - - +
26B LEU* 1.3 62.0 - - - +
27B ILE* 3.6 18.0 + - + +
36B GLU* 3.6 1.6 - - - -
37B GLN* 2.9 55.4 + - + +
287B ALA* 4.1 5.6 - - + -
288B GLY 3.5 25.6 + - - -
289B LEU 4.2 9.6 + - - -
290B ASP 5.5 0.4 - - - -
291B GLY* 4.0 17.9 - - - -
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Residues in contact with LEU 26 (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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19B SER 5.0 0.6 + - - -
24B PHE* 3.8 10.0 - - + -
25B HIS* 1.3 72.6 - - - +
27B ILE* 1.3 57.4 + - - +
28B ASP 3.4 21.5 - - - +
29B SER* 4.6 4.7 - - - +
34B LYS* 3.9 22.0 - - + -
35B LEU 3.6 7.9 - - - +
36B GLU* 3.9 10.3 - - + +
284B ILE* 3.8 24.3 - - + +
285B ARG 4.3 2.0 + - - +
286B GLU* 3.5 37.7 - - + +
287B ALA* 2.8 33.4 + - - +
288B GLY 3.7 0.7 + - - -
296B ARG 5.0 0.2 - - - +
298B LEU* 4.1 29.8 - - + -
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Residues in contact with ILE 27 (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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25B HIS* 3.6 22.2 + - + +
26B LEU* 1.3 73.6 - - - +
28B ASP* 1.3 62.7 + - + +
35B LEU* 2.7 31.7 + - + +
36B GLU 4.1 2.0 - - - -
37B GLN* 3.7 20.6 - - + +
42B ARG* 3.3 46.9 - - + +
56B VAL* 4.3 6.1 - - + +
286B GLU* 4.3 5.4 - - - +
288B GLY* 3.3 26.0 + - - +
289B LEU* 3.8 34.8 - - + +
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Residues in contact with ASP 28 (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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26B LEU* 3.4 6.9 - - - +
27B ILE* 1.3 84.6 - - + +
29B SER* 1.3 75.0 + - - +
35B LEU* 2.8 27.1 + - + +
54B PRO* 3.2 3.6 - - - +
55B LEU* 2.9 27.4 + - - +
56B VAL* 2.9 36.8 + - + +
61B TRP* 3.0 28.1 + - + +
286B GLU* 3.6 9.5 - - - +
296B ARG* 3.4 10.7 + - - -
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Residues in contact with SER 29 (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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26B LEU* 4.6 9.0 - - - +
28B ASP* 1.3 78.4 - - - +
30B GLY* 1.3 58.9 + - - +
33B LEU 3.3 13.9 - - - -
34B LYS* 4.2 8.5 - - - -
50B ALA* 4.0 8.7 - - - -
52B TRP* 2.8 26.2 + - - -
54B PRO* 3.2 11.6 - - - +
61B TRP* 3.9 6.5 - - - -
286B GLU* 2.7 24.6 + - - +
296B ARG* 3.0 22.5 + - - -
298B LEU* 5.4 2.7 - - - -
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Residues in contact with GLY 30 (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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29B SER* 1.3 75.9 - - - +
31B ASN* 1.3 73.7 + - - +
32B GLY 3.0 3.6 - - - -
33B LEU* 2.9 24.2 + - - +
50B ALA* 3.4 9.0 - - - +
52B TRP* 2.9 20.0 - - - -
54B PRO* 3.8 12.4 - - - +
61B TRP* 4.3 2.1 - - - -
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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