Contacts of the strand formed by residues 160 - 166 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1537 LEU* 4.4 6.3 - - + -
1547 ASP 3.2 9.4 - - - +
1557 SER* 2.6 25.1 + - - +
1597 VAL* 1.4 72.2 - - - +
1617 HIS* 1.3 74.6 + - - +
1627 ASN* 5.0 2.9 - - - +
1777 ARG* 3.3 5.9 - - - +
1787 LEU* 2.9 46.3 + - + -
1807 LEU 3.1 16.7 + - - -
1817 ALA* 4.3 0.2 - - - +
2617 LEU* 5.1 0.3 - - - +
2747 ILE* 3.6 32.0 - - + +
2777 THR* 6.1 0.2 - - + -
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Residues in contact with HIS 161 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737 HIS 5.2 0.7 - - - -
1087 ALA* 4.9 7.0 - - + -
1097 PRO* 3.6 41.2 - - + +
1107 LEU* 5.2 3.8 + - - +
1527 VAL 4.1 0.2 - - - -
1537 LEU* 3.4 4.7 - - - +
1547 ASP* 2.7 41.7 + - + +
1597 VAL* 4.0 31.6 - - + +
1607 THR* 1.3 80.4 + - - +
1627 ASN* 1.3 66.4 + - - +
1637 VAL* 4.2 11.2 - - + -
1757 ILE* 4.0 8.7 - - + +
1767 MET 3.0 17.3 - - - -
1777 ARG* 3.7 28.4 + - + +
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Residues in contact with ASN 162 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517 ILE* 4.5 6.0 - - + +
1527 VAL 3.2 6.9 + - - +
1537 LEU* 3.6 21.3 - - - +
1607 THR* 5.0 2.3 - - - +
1617 HIS* 1.3 75.1 + - - +
1637 VAL* 1.3 63.6 + - - +
1647 PRO* 3.5 1.6 - - - +
1757 ILE* 3.2 25.1 - - - +
1767 MET* 2.9 14.5 + - + +
1787 LEU* 5.8 0.5 + - - +
2777 THR* 2.9 30.9 - - - +
2787 THR* 3.4 34.6 + - - +
2817 SER* 3.6 20.0 - - - +
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Residues in contact with VAL 163 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097 PRO* 3.5 33.4 - - + -
1367 ILE* 5.1 2.5 - - + -
1387 ALA* 3.4 21.8 - - + -
1397 VAL* 5.0 0.9 - - + -
1517 ILE* 4.2 0.6 - - - +
1527 VAL* 2.9 28.7 + - - +
1547 ASP* 5.8 0.7 - - + -
1617 HIS* 4.2 9.2 - - + -
1627 ASN* 1.3 78.1 - - - +
1647 PRO* 1.3 62.6 - - - +
1657 ILE* 3.5 17.0 + - + +
1707 ALA* 3.6 30.5 - - + -
1757 ILE* 3.9 15.9 - - + -
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Residues in contact with PRO 164 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1507 GLY 3.7 6.7 - - - +
1517 ILE* 3.9 16.2 - - + -
1627 ASN 3.5 7.0 - - - +
1637 VAL* 1.3 84.0 - - - +
1657 ILE* 1.3 59.8 + - - +
1707 ALA* 3.6 0.3 - - - -
1717 LEU* 2.8 36.3 + - + +
1747 ALA* 3.7 15.9 - - + -
1757 ILE* 4.0 18.4 - - + +
2817 SER* 3.4 20.9 - - - +
2857 CYS* 3.8 20.6 - - - -
2937 LEU* 4.4 9.0 - - + -
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Residues in contact with ILE 165 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1387 ALA* 3.7 9.6 - - + +
1397 VAL* 3.5 40.6 - - + +
1427 LEU* 3.9 18.2 - - + -
1487 THR 3.4 16.6 - - - +
1497 THR* 3.1 23.9 - - - +
1507 GLY 2.9 13.1 + - - +
1527 VAL* 4.5 2.9 - - + -
1637 VAL* 3.5 21.1 + - + +
1647 PRO* 1.3 73.6 - - - +
1667 TYR* 1.3 61.6 + - - +
1687 GLY* 3.6 25.8 - - - +
1697 TYR 3.7 3.1 - - - +
1707 ALA* 3.6 16.2 - - + -
1717 LEU* 4.7 1.3 - - - -
2937 LEU* 4.3 2.5 - - - +
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Residues in contact with TYR 166 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1497 THR* 3.6 18.6 - - + -
1647 PRO 4.4 0.2 - - - -
1657 ILE* 1.3 72.1 - - - +
1677 GLU* 1.3 90.5 + - + +
1687 GLY 2.9 4.8 + - - -
1697 TYR* 3.1 26.5 + - + +
1717 LEU* 4.3 21.3 - - + +
2897 ILE* 3.7 36.6 - - + -
2927 ASP* 4.0 17.0 + - - -
449 MET* 5.9 1.3 - - + -
609 SER 4.8 9.2 + - - -
619 LYS* 6.1 2.1 - - + +
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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