Contacts of the strand formed by residues 491 - 498 (chain 0) in PDB entry 5OA3
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 ILE 491 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4890 CYS 3.8 0.8 + - - -
4900 PRO* 1.3 68.7 - - - +
4920 ASP* 1.3 59.9 + - - +
4930 ILE* 3.8 3.2 + - + -
5070 VAL* 3.6 24.2 - - + -
5080 ARG 3.2 16.2 - - - +
5090 ASN 3.3 18.6 - - - +
5100 LEU* 3.7 20.9 - - + -
5130 TYR* 3.5 26.2 - - + -
5150 LEU* 4.2 4.9 - - + -
5600 LEU* 4.6 17.0 - - + -
5660 LEU* 4.2 21.5 - - + -
5700 HIS 2.8 14.9 + - - +
5710 ILE* 3.8 6.3 - - + +
5720 GLN* 3.1 25.6 + - - +
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Residues in contact with ASP 492 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4900 PRO* 3.2 7.5 + - + +
4910 ILE* 1.3 72.8 - - - +
4930 ILE* 1.3 62.2 + - - +
4940 THR* 3.2 27.8 + - - +
5060 VAL 3.3 5.2 - - - +
5070 VAL* 3.5 0.2 - - - -
5080 ARG* 2.9 61.5 + - + +
5090 ASN* 5.1 4.7 - - - +
5720 GLN* 4.2 18.5 - - + +
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Residues in contact with ILE 493 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4910 ILE* 4.6 3.6 - - + +
4920 ASP* 1.3 76.0 + - - +
4940 THR* 1.3 66.9 + - - +
4950 LEU* 5.0 2.0 - - + +
5050 THR* 3.8 25.6 - - + -
5060 VAL 3.4 3.1 - - - +
5070 VAL* 4.3 16.4 - - + -
5530 VAL* 4.0 18.6 - - + -
5560 LEU* 4.0 24.5 - - + -
5600 LEU* 4.2 7.9 - - + -
5710 ILE* 3.8 26.5 - - + -
5720 GLN 3.3 22.2 + - - +
5730 GLY* 4.0 15.1 - - - +
5740 LEU* 3.9 14.8 - - + -
5760 LYS* 5.9 2.1 - - - +
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Residues in contact with THR 494 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4920 ASP* 3.2 29.0 + - - +
4930 ILE* 1.3 76.8 - - - +
4950 LEU* 1.3 68.3 + - - +
4960 ALA* 4.1 2.6 + - - +
5040 VAL 3.7 0.7 - - - +
5050 THR* 3.6 0.9 - - - +
5060 VAL* 2.9 53.9 + - - +
5080 ARG* 4.4 13.6 + - - +
5760 LYS* 6.2 3.6 - - - +
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Residues in contact with LEU 495 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4930 ILE* 5.0 3.1 - - + +
4940 THR* 1.3 82.5 - - - +
4960 ALA* 1.3 61.9 + - - +
4970 GLN* 4.4 1.0 + - - +
5030 LYS* 3.9 20.3 - - - +
5040 VAL 3.5 2.0 - - - +
5050 THR* 3.3 30.7 - - + +
5500 GLY 5.2 0.2 - - - +
5510 ASN* 3.7 21.8 - - - +
5530 VAL* 3.6 23.6 - - + -
5730 GLY 5.9 1.3 - - - +
5760 LYS* 3.6 47.6 + - + +
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Residues in contact with ALA 496 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4940 THR* 4.1 2.7 + - - +
4950 LEU* 1.3 76.2 - - - +
4970 GLN* 1.3 64.4 - - - +
4980 ARG* 3.7 27.9 + - + +
5030 LYS* 3.5 5.4 - - - +
5040 VAL* 2.9 38.0 + - + +
5060 VAL* 5.4 4.5 - - + -
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Residues in contact with GLN 497 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4950 LEU 5.6 1.3 - - - +
4960 ALA* 1.3 72.8 - - - +
4980 ARG* 1.3 62.0 + - - +
5010 ASN* 5.2 5.5 - - - -
5020 LYS 4.2 4.0 + - - +
5030 LYS* 3.3 51.1 + - - +
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Residues in contact with ARG 498 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4960 ALA* 3.7 21.0 + - + +
4970 GLN* 1.3 79.5 - - - +
4990 ALA* 1.3 74.0 + - + +
5010 ASN 3.9 1.2 + - - -
5020 LYS* 2.9 36.3 + - + +
5040 VAL* 3.7 25.9 - - + +
5060 VAL* 4.0 20.6 - - - +
5080 ARG* 6.0 1.6 - - - +
5450 GLN* 4.7 3.8 - - - +
5470 GLN* 3.2 33.8 + - - +
10582 A 4.7 22.4 + - - +
10592 G 5.7 1.8 + - - -
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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