Contacts of the strand formed by residues 160 - 166 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1534 LEU* 4.4 6.7 - - + -
1544 ASP 3.2 9.4 - - - +
1554 SER* 2.6 26.2 + - - +
1594 VAL* 1.4 71.3 - - - +
1614 HIS* 1.3 73.9 + - - +
1624 ASN* 5.0 2.5 - - - +
1774 ARG* 3.3 7.1 - - - +
1784 LEU* 2.9 46.7 + - + +
1804 LEU 3.1 16.4 + - - -
2614 LEU* 5.1 0.3 - - - +
2744 ILE* 3.6 30.6 - - + +
2774 THR* 6.1 0.4 - - + -
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Residues in contact with HIS 161 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734 HIS 5.2 0.7 - - - -
1084 ALA* 4.9 7.6 - - + -
1094 PRO* 3.6 41.4 - - + +
1104 LEU* 5.2 3.2 + - - +
1524 VAL 4.1 0.4 - - - -
1534 LEU* 3.4 4.7 - - - -
1544 ASP* 2.7 41.3 + - + +
1594 VAL* 4.0 32.8 - - + +
1604 THR* 1.3 80.3 + - - +
1624 ASN* 1.3 65.8 + - - +
1634 VAL* 4.2 11.4 - - + -
1754 ILE* 4.0 8.2 - - + +
1764 MET 3.0 17.3 - - - -
1774 ARG* 3.7 28.8 + - + +
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Residues in contact with ASN 162 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514 ILE* 4.5 5.9 - - + +
1524 VAL 3.2 6.9 + - - -
1534 LEU* 3.6 20.8 - - - +
1604 THR* 5.0 2.3 - - - +
1614 HIS* 1.3 75.7 + - - +
1634 VAL* 1.3 63.5 + - - +
1644 PRO* 3.5 1.8 - - - +
1754 ILE* 3.2 24.1 - - - +
1764 MET* 2.9 13.3 + - + +
1784 LEU* 5.8 0.5 + - - +
2774 THR* 2.9 32.2 - - - +
2784 THR* 3.4 34.1 + - - +
2814 SER* 3.6 20.0 - - - +
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Residues in contact with VAL 163 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094 PRO* 3.5 34.5 - - + -
1364 ILE* 5.1 2.2 - - + -
1384 ALA* 3.4 22.0 - - + -
1394 VAL* 5.0 1.1 - - + -
1514 ILE* 4.2 1.1 - - - +
1524 VAL 2.9 28.0 + - - +
1544 ASP* 5.8 0.7 - - + -
1614 HIS* 4.2 9.4 - - + -
1624 ASN* 1.3 79.2 - - - +
1644 PRO* 1.3 62.0 - - - +
1654 ILE* 3.5 18.2 + - + +
1704 ALA* 3.6 30.7 - - + -
1754 ILE* 3.9 15.5 - - + -
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Residues in contact with PRO 164 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504 GLY 3.7 7.2 - - - +
1514 ILE* 3.9 16.2 - - + -
1624 ASN 3.5 7.4 - - - +
1634 VAL* 1.3 83.2 - - - +
1654 ILE* 1.3 59.7 + - - +
1704 ALA* 3.6 0.3 - - - -
1714 LEU* 2.8 37.0 + - + +
1744 ALA* 3.7 15.3 - - + -
1754 ILE* 4.0 17.3 - - + +
2814 SER* 3.4 20.9 - - - +
2854 CYS* 3.8 20.9 - - - -
2934 LEU* 4.4 9.0 - - + -
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Residues in contact with ILE 165 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384 ALA* 3.7 9.2 - - + +
1394 VAL* 3.5 40.6 - - + +
1424 LEU* 3.9 19.3 - - + -
1484 THR* 3.4 16.8 - - - +
1494 THR* 3.1 23.7 - - - +
1504 GLY 2.9 13.3 + - - +
1524 VAL* 4.5 2.5 - - + -
1634 VAL* 3.6 20.9 - - + +
1644 PRO* 1.3 75.8 - - - +
1664 TYR* 1.3 60.8 + - - +
1684 GLY* 3.6 25.4 - - - +
1694 TYR 3.7 2.7 - - - +
1704 ALA* 3.6 15.5 - - + -
1714 LEU* 4.7 1.1 - - - -
2934 LEU* 4.3 2.0 - - - +
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Residues in contact with TYR 166 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494 THR* 3.6 18.6 - - + -
1654 ILE* 1.3 72.7 - - - +
1674 GLU* 1.3 90.2 + - + +
1684 GLY 2.9 4.8 + - - -
1694 TYR* 3.1 26.3 + - + +
1714 LEU* 4.3 20.6 - - + +
2894 ILE* 3.7 35.4 - - + -
2924 ASP* 4.0 17.0 + - - -
446 MET* 5.0 8.1 - - - +
606 SER 5.1 5.2 + - - -
616 LYS* 5.1 12.6 - - - +
646 ILE* 4.9 28.5 - - + -
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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