Contacts of the strand formed by residues 160 - 166 (chain 3) in PDB entry 1MVW
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 THR 160 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1533 LEU* 4.4 6.3 - - + -
1543 ASP 3.2 9.2 - - - +
1553 SER* 2.6 24.8 + - - +
1593 VAL* 1.4 71.8 - - - +
1613 HIS* 1.3 75.8 + - - +
1623 ASN* 5.0 3.1 - - - +
1773 ARG* 3.3 6.1 - - - +
1783 LEU* 2.9 45.6 + - + -
1803 LEU 3.1 16.9 + - - -
1813 ALA* 4.3 0.2 - - - +
2613 LEU* 5.1 0.3 - - - +
2743 ILE* 3.6 31.4 - - + +
2773 THR* 6.1 0.4 - - + -
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Residues in contact with HIS 161 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733 HIS 5.2 1.1 - - - -
1083 ALA* 4.9 7.6 - - + -
1093 PRO* 3.6 40.9 - - + +
1103 LEU* 5.2 3.8 + - - +
1523 VAL 4.1 0.2 - - - -
1533 LEU* 3.4 4.7 - - - -
1543 ASP* 2.7 40.7 + - + +
1593 VAL* 4.0 32.1 - - + +
1603 THR* 1.3 80.8 + - - +
1623 ASN* 1.3 67.9 + - - +
1633 VAL* 4.2 11.9 - - + -
1753 ILE* 4.0 8.0 - - + +
1763 MET 3.0 17.3 - - - -
1773 ARG* 3.7 28.6 + - + +
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Residues in contact with ASN 162 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513 ILE* 4.5 6.0 - - + +
1523 VAL 3.2 6.7 + - - +
1533 LEU* 3.6 21.0 - - - +
1603 THR* 5.0 2.1 - - - +
1613 HIS* 1.3 75.1 + - - +
1633 VAL* 1.3 61.8 + - - +
1643 PRO* 3.5 2.7 - - - +
1753 ILE* 3.2 25.1 - - - +
1763 MET* 2.9 15.2 + - + +
1783 LEU* 5.8 0.3 + - - +
2773 THR* 2.9 30.7 - - - +
2783 THR* 3.4 34.8 + - - +
2813 SER* 3.6 20.6 - - - +
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Residues in contact with VAL 163 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 PRO* 3.5 33.7 - - + -
1363 ILE* 5.1 2.5 - - + -
1383 ALA* 3.4 22.4 - - + -
1393 VAL* 5.0 0.9 - - + -
1513 ILE* 4.2 0.6 - - - +
1523 VAL 2.9 28.2 + - - +
1613 HIS* 4.2 10.3 - - + -
1623 ASN* 1.3 79.3 - - - +
1643 PRO* 1.3 62.6 - - - +
1653 ILE* 3.5 17.0 + - + +
1703 ALA* 3.6 31.2 - - + -
1753 ILE* 3.9 15.5 - - + -
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Residues in contact with PRO 164 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503 GLY 3.7 7.0 - - - +
1513 ILE* 3.9 15.5 - - + -
1623 ASN 3.5 7.0 - - - +
1633 VAL* 1.3 82.9 - - - +
1653 ILE* 1.3 59.4 + - - +
1703 ALA* 3.6 0.3 - - - -
1713 LEU* 2.8 35.4 + - + +
1743 ALA* 3.7 15.9 - - + -
1753 ILE* 4.0 18.2 - - + +
2813 SER* 3.4 20.4 - - - +
2853 CYS* 3.8 21.5 - - - -
2933 LEU* 4.4 9.0 - - + -
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Residues in contact with ILE 165 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383 ALA* 3.7 9.4 - - + +
1393 VAL* 3.5 40.8 - - + +
1423 LEU* 3.9 18.4 - - + -
1483 THR 3.4 16.6 - - - +
1493 THR* 3.1 24.1 - - - +
1503 GLY 2.9 13.3 + - - +
1523 VAL* 4.5 2.9 - - + -
1633 VAL* 3.6 20.9 - - + +
1643 PRO* 1.3 73.8 - - - +
1663 TYR* 1.3 61.8 + - - +
1683 GLY* 3.6 25.8 - - - +
1693 TYR 3.7 2.9 - - - -
1703 ALA* 3.6 16.2 - - + -
1713 LEU* 4.7 1.3 - - - -
2933 LEU* 4.3 1.9 - - - +
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Residues in contact with TYR 166 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493 THR* 3.6 17.9 - - + -
1653 ILE* 1.3 72.8 - - - +
1673 GLU* 1.3 89.9 + - + +
1683 GLY 2.9 4.8 + - - -
1693 TYR* 3.1 26.5 + - + +
1713 LEU* 4.3 21.0 - - + +
2893 ILE* 3.7 35.7 - - + -
2923 ASP* 4.0 17.5 + - - -
445 MET* 5.2 7.1 - - - +
605 SER 4.9 9.2 + - - -
615 LYS* 5.2 8.6 - - + +
645 ILE* 5.4 22.0 - - + -
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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