Contacts of the strand formed by residues 131 - 136 (chain 2) 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 ALA 131 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022 PRO* 3.2 13.1 - - + +
1032 THR 2.9 21.6 + - - -
1242 PHE* 3.8 3.6 - - - -
1292 VAL* 3.4 6.3 - - - +
1302 PRO* 1.3 83.1 - - + +
1322 MET* 1.3 64.9 + - - +
3562 TRP* 4.0 21.5 - - + -
3572 ILE 3.0 19.7 - - - +
3582 THR* 3.9 9.9 - - + -
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Residues in contact with MET 132 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032 THR* 3.2 18.6 - - - +
1052 LEU* 3.7 15.9 - - + -
1192 MET 4.0 0.7 - - - +
1202 THR* 3.8 28.5 - - - +
1232 MET* 3.6 36.1 - - + -
1242 PHE* 3.4 33.9 - - + -
1292 VAL* 4.2 6.7 - - + -
1312 ALA* 1.3 75.0 - - - +
1332 TYR* 1.3 64.6 + - - +
1342 VAL* 4.1 10.3 - - + -
3562 TRP* 3.4 6.1 - - - -
3572 ILE* 2.8 30.9 + - - +
3702 VAL* 4.3 11.2 - - - -
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Residues in contact with TYR 133 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032 THR 3.3 2.0 + - - -
1042 LEU* 3.5 15.5 - - + +
1052 LEU* 2.8 27.7 + - - +
1322 MET* 1.3 81.8 - - - +
1342 VAL* 1.3 74.8 + - - +
1352 ALA* 4.2 13.0 - - + -
3462 LEU* 4.5 4.3 - - + -
3522 PHE* 3.3 32.5 - + + -
3552 MET* 3.5 42.2 - - + +
3562 TRP* 3.9 16.2 - - + -
3572 ILE* 5.1 2.7 - - + -
3702 VAL* 4.7 4.9 - - + -
3722 ARG* 2.9 43.6 + - - -
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Residues in contact with VAL 134 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052 LEU* 3.4 5.2 - - + -
1062 THR 4.4 2.7 - - - -
1072 GLU* 3.6 47.6 - - + +
1162 ARG* 3.2 41.9 + - + +
1192 MET* 4.3 18.6 - - + -
1202 THR* 4.5 6.5 - - - +
1322 MET* 4.1 21.1 - - + -
1332 TYR* 1.3 85.6 - - - +
1352 ALA* 1.3 56.7 + - - +
3702 VAL* 4.6 9.2 - - + +
3722 ARG* 4.5 3.6 + - - +
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Residues in contact with ALA 135 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042 LEU* 4.2 7.2 - - + -
1052 LEU 2.9 11.1 + - - +
1062 THR* 3.3 4.9 - - - -
1072 GLU* 3.0 22.7 + - - +
1162 ARG* 4.9 0.4 - - - +
1332 TYR* 4.0 18.6 - - + -
1342 VAL* 1.3 71.9 - - - +
1362 ILE* 1.3 62.3 + - - +
1392 VAL* 6.1 1.6 - - + -
1402 LEU* 3.6 38.8 - - + -
3462 LEU* 4.7 1.6 - - + -
3722 ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 136 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072 GLU* 3.7 25.4 - - + +
1082 ALA 4.6 2.5 - - - +
1092 PRO* 4.2 32.3 - - + +
1162 ARG* 4.0 14.4 - - - +
1342 VAL 4.3 0.2 + - - -
1352 ALA* 1.3 72.3 - - - +
1372 GLN* 1.3 69.6 + - - +
1382 ALA* 4.2 7.9 - - + +
1392 VAL* 3.2 38.3 + - + +
1402 LEU* 3.2 11.2 + - - +
1632 VAL* 5.1 1.3 - - + -
1702 ALA* 4.8 14.6 - - + -
1752 ILE* 6.5 0.2 - - + -
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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