Contacts of the strand formed by residues 18 - 25 (chain D) in PDB entry 3IT8
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 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D THR 3.6 0.6 - - - +
9D VAL* 2.9 7.4 - - - +
10D THR* 2.8 38.3 + - - +
12D LYS* 3.0 40.5 - - + +
16D LEU* 4.0 1.9 + - - -
17D TYR* 1.3 75.9 - - - +
19D GLY* 1.3 62.0 + - - +
20D VAL* 5.9 1.8 - - + -
35D TYR 4.7 3.5 - - - +
37D HIS* 2.9 27.4 + - - -
70D TYR* 4.0 1.8 - - - -
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Residues in contact with GLY 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR 3.2 7.0 - - - -
9D VAL* 4.2 0.7 - - - -
18D ASP* 1.3 79.0 + - - +
20D VAL* 1.3 67.2 + - - +
34D SER* 3.1 5.9 - - - -
35D TYR* 2.9 28.4 + - - +
66D PHE* 3.9 7.6 - - - -
70D TYR* 3.8 24.1 - - - -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN 3.7 0.6 - - - +
7D TYR* 3.5 1.9 - - - -
8D THR* 2.8 51.8 + - + +
10D THR* 5.7 2.2 - - - +
18D ASP* 5.9 1.8 - - + -
19D GLY* 1.3 79.7 - - - +
21D PHE* 1.3 62.5 + - - +
22D TYR* 4.2 24.7 - - + +
32D LYS* 4.5 15.0 - - - -
33D ILE 3.1 10.8 - - - +
34D SER* 4.0 11.2 - - - -
66D PHE* 3.9 5.9 - - - -
325D NAG 4.4 8.3 - - - -
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Residues in contact with PHE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.9 16.6 - + + -
6D ASN 3.1 15.7 - - - -
7D TYR* 3.4 43.5 - + + -
20D VAL* 1.3 76.1 - - - +
22D TYR* 1.3 82.9 + - - +
23D ASP* 3.8 13.7 - - + -
31D THR* 4.3 4.3 - - + -
32D LYS* 3.3 7.3 - - - +
33D ILE* 2.7 50.9 + - + +
64D TYR* 3.2 46.4 - + + -
66D PHE* 3.7 21.8 - + + -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LYS 3.6 1.4 - - - +
5D TYR* 3.5 5.4 - - - -
6D ASN* 2.9 42.9 + - + +
20D VAL* 4.2 18.7 - - + +
21D PHE* 1.3 84.7 - - - +
23D ASP* 1.3 60.0 + - - +
24D HIS* 3.9 24.6 - - + -
29D LEU* 3.9 21.1 - - + -
31D THR 3.4 1.8 - - - -
32D LYS* 3.7 41.4 + - + -
325D NAG 3.0 40.2 + - - -
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Residues in contact with ASP 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.6 5.0 - - - +
4D LYS 3.6 3.1 - - - -
5D TYR* 3.2 16.1 - - - -
21D PHE* 3.8 9.0 - - + -
22D TYR* 1.3 73.1 - - - +
24D HIS* 1.3 59.0 + - - +
29D LEU* 3.6 3.6 - - - +
30D VAL* 2.7 40.5 + - - +
31D THR* 2.9 28.4 + - - +
64D TYR* 2.9 23.0 + - - -
170D TYR* 2.7 35.8 + - - -
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Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR 3.7 0.5 - - - +
3D LEU* 3.5 4.0 - - - +
4D LYS* 2.8 68.9 + - + +
6D ASN* 5.9 0.7 - - + -
22D TYR* 3.9 31.5 - + + +
23D ASP* 1.3 75.2 + - - +
25D TYR* 1.3 61.0 + - - +
26D ASN 3.8 13.3 + - - +
27D ASP* 4.4 8.7 + - - -
28D GLN 3.4 3.1 - - - -
29D LEU* 3.4 40.9 + - + +
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Residues in contact with TYR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ILE* 3.1 30.3 - - + +
2D THR 3.3 15.7 - - - -
3D LEU* 4.4 2.7 - - + -
24D HIS* 1.3 71.2 - - - +
26D ASN* 1.3 81.3 + - - +
28D GLN* 2.8 33.3 + - + +
30D VAL* 3.8 19.5 - - + +
50D TRP* 4.1 9.2 - + + -
167D ILE* 4.1 17.5 - - + -
170D TYR* 3.5 32.5 - + + -
171D GLN* 3.4 27.7 - - - +
174D ALA* 3.7 28.5 - - + -
178D ILE* 3.9 8.7 - - + -
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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