Contacts of the strand formed by residues 160 - 166 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1531 LEU* 4.4 6.1 - - + -
1541 ASP 3.2 9.4 - - - +
1551 SER* 2.6 26.0 + - - +
1591 VAL* 1.4 70.9 - - - +
1611 HIS* 1.3 76.5 + - - +
1621 ASN* 5.0 2.7 - - - +
1771 ARG* 3.3 6.8 - - - +
1781 LEU* 2.9 46.3 + - + -
1801 LEU 3.1 16.3 + - - -
2611 LEU* 5.1 0.2 - - - +
2741 ILE* 3.6 31.0 - - + +
2771 THR* 6.1 0.7 - - + -
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Residues in contact with HIS 161 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731 HIS 5.2 0.9 - - - -
1081 ALA* 4.9 7.2 - - + -
1091 PRO* 3.6 41.9 - - + +
1101 LEU* 5.2 3.0 + - - +
1521 VAL 4.1 0.2 - - - -
1531 LEU* 3.4 4.9 - - - -
1541 ASP* 2.7 40.5 + - + +
1591 VAL* 4.0 31.3 - - + +
1601 THR* 1.3 80.4 + - - +
1621 ASN* 1.3 67.2 + - - +
1631 VAL* 4.2 11.0 - - + -
1751 ILE* 4.0 8.4 - - + +
1761 MET 3.0 17.0 - - - -
1771 ARG* 3.7 28.8 + - + +
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Residues in contact with ASN 162 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511 ILE* 4.5 5.4 - - + +
1521 VAL 3.2 7.4 + - - +
1531 LEU* 3.6 21.0 - - - +
1601 THR* 5.0 2.1 - - - +
1611 HIS* 1.3 75.6 + - - +
1631 VAL* 1.3 63.4 + - - +
1641 PRO* 3.5 2.4 - - - +
1751 ILE* 3.2 24.4 - - - +
1761 MET 2.9 12.9 + - - +
1781 LEU* 5.8 0.3 + - - +
2771 THR* 2.9 31.9 - - - +
2781 THR* 3.4 34.4 + - - +
2811 SER* 3.6 20.9 - - - +
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Residues in contact with VAL 163 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091 PRO* 3.5 35.2 - - + -
1361 ILE* 5.1 2.0 - - + -
1381 ALA* 3.4 20.4 - - + -
1391 VAL* 5.0 0.9 - - + -
1511 ILE* 4.2 1.1 - - - +
1521 VAL 2.9 28.4 + - - +
1541 ASP* 5.8 0.4 - - + -
1611 HIS* 4.2 9.4 - - + -
1621 ASN* 1.3 77.6 - - - +
1641 PRO* 1.3 62.6 - - - +
1651 ILE* 3.5 17.2 + - + +
1701 ALA* 3.6 31.4 - - + -
1751 ILE* 3.9 16.2 - - + -
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Residues in contact with PRO 164 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501 GLY 3.7 6.5 - - - +
1511 ILE* 3.9 16.6 - - + -
1621 ASN 3.5 7.2 - - - +
1631 VAL* 1.3 82.2 - - - +
1651 ILE* 1.3 60.3 + - - +
1701 ALA* 3.6 0.3 - - - -
1711 LEU* 2.8 36.4 + - + +
1741 ALA* 3.7 15.5 - - + -
1751 ILE* 4.0 17.9 - - + +
2811 SER* 3.4 21.3 - - - +
2851 CYS* 3.8 21.3 - - - -
2931 LEU* 4.4 9.2 - - + -
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Residues in contact with ILE 165 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381 ALA* 3.7 9.2 - - + +
1391 VAL* 3.5 40.8 - - + +
1421 LEU* 3.9 19.3 - - + -
1481 THR 3.4 17.3 - - - +
1491 THR* 3.1 23.7 - - - +
1501 GLY 2.9 12.7 + - - +
1521 VAL* 4.5 2.7 - - + -
1631 VAL* 3.6 20.6 - - + +
1641 PRO* 1.3 75.1 - - - +
1661 TYR* 1.3 63.1 + - - +
1681 GLY* 3.6 25.6 - - - +
1691 TYR 3.7 2.9 - - - +
1701 ALA* 3.6 15.7 - - + -
1711 LEU* 4.7 1.1 - - - -
2931 LEU* 4.3 2.2 - - - +
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Residues in contact with TYR 166 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491 THR* 3.6 19.3 - - + -
1651 ILE* 1.3 73.2 - - - +
1671 GLU* 1.3 89.2 + - + +
1681 GLY 2.9 4.6 + - - -
1691 TYR* 3.1 26.5 + - + +
1711 LEU* 4.3 21.0 - - + +
2891 ILE* 3.7 26.9 - - + -
2921 ASP* 4.0 17.0 + - - -
403 HIS* 4.4 26.0 - + + +
443 MET* 6.0 0.2 - - - -
643 ILE* 2.2 67.0 - - + +
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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