Contacts of the strand formed by residues 24 - 30 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 5.8 2.2 - - - -
20A GLY* 3.1 35.4 - - - -
21A ALA 3.1 4.8 + - - +
22A GLY 3.3 0.4 - - - -
23A ASP* 1.3 81.6 - - - +
25A HIS* 1.3 88.8 + - - +
26A LEU* 3.8 16.6 - - + -
36A GLU* 3.6 18.4 - - + -
37A GLN 3.2 9.6 - - - -
38A TYR* 3.4 38.6 - + + -
95A LEU* 4.2 11.8 - - + +
114A PRO* 3.5 33.7 - - + -
115A GLU* 5.1 1.8 - - - -
284A ILE* 4.1 34.3 - - + -
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Residues in contact with HIS 25 (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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19A SER 4.0 8.7 - - - +
20A GLY* 4.1 5.1 + - - +
21A ALA 6.1 0.2 - - - -
22A GLY 4.9 7.5 + - - -
23A ASP 5.7 0.2 - - - -
24A PHE* 1.3 92.9 + - - +
26A LEU* 1.3 61.4 + - - +
27A ILE* 3.5 26.0 + - + +
36A GLU* 3.5 1.6 - - - -
37A GLN* 2.9 51.1 + - + +
42A ARG* 5.2 3.4 + - - -
287A ALA* 3.9 23.1 - - + -
288A GLY 3.8 16.3 + - - -
289A LEU 4.3 9.6 + - - -
292A LYS* 4.5 1.6 - - - +
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Residues in contact with LEU 26 (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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19A SER 5.3 0.4 + - - -
24A PHE* 3.8 9.4 - - + -
25A HIS* 1.3 71.8 - - - +
27A ILE* 1.3 57.0 + - - +
28A ASP 3.4 22.9 - - - +
29A SER* 4.5 4.0 - - - +
34A LYS* 3.9 22.2 - - + -
35A LEU 3.7 7.0 - - - +
36A GLU* 4.0 9.6 - - + +
284A ILE* 3.8 27.7 - - + +
285A ARG 4.4 1.0 + - - +
286A GLU* 3.4 36.3 - - + +
287A ALA* 2.6 35.4 + - - +
296A ARG 5.1 0.2 - - - +
298A LEU* 4.1 26.7 - - + -
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Residues in contact with ILE 27 (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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25A HIS* 3.6 23.6 - - + +
26A LEU* 1.3 72.3 - - - +
28A ASP* 1.3 57.9 + - - +
35A LEU* 2.8 33.4 + - + +
37A GLN* 3.8 17.7 - - + +
42A ARG* 3.1 48.5 - - + +
56A VAL* 3.9 10.2 - - + +
286A GLU* 4.4 4.0 - - - +
287A ALA 4.4 0.3 + - - -
288A GLY* 3.2 36.8 + - - +
289A LEU* 3.8 25.8 - - + -
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Residues in contact with ASP 28 (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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26A LEU* 3.4 7.5 - - - +
27A ILE* 1.3 84.2 - - + +
29A SER* 1.3 73.8 + - - +
35A LEU* 2.8 26.3 + - + +
54A PRO* 3.2 4.7 - - - +
55A LEU* 2.8 28.4 + - - +
56A VAL* 2.9 31.7 + - + +
61A TRP* 2.8 36.1 + - + +
286A GLU* 3.7 8.9 - - - +
296A ARG* 3.4 10.0 + - - -
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Residues in contact with SER 29 (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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26A LEU* 4.5 8.7 - - - +
28A ASP* 1.3 80.8 + - - +
30A GLY* 1.3 59.0 + - - +
33A LEU 3.3 14.6 - - - -
34A LYS* 4.1 9.6 - - - -
50A ALA* 4.1 8.1 - - - -
52A TRP* 2.8 26.4 + - - -
54A PRO* 3.3 11.1 - - - +
61A TRP* 3.9 6.1 - - - -
286A GLU* 2.6 23.2 + - - +
296A ARG* 3.1 22.5 + - - -
298A LEU* 5.5 2.9 - - - -
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Residues in contact with GLY 30 (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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29A SER* 1.3 75.7 - - - +
31A ASN* 1.3 74.0 + - - +
32A GLY 3.1 3.1 - - - -
33A LEU* 2.9 24.6 + - - +
50A ALA* 3.5 8.3 - - - +
52A TRP* 3.0 20.6 - - - -
54A PRO* 3.9 11.0 - - - +
61A TRP* 4.4 1.6 - - - -
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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