Contacts of the helix formed by residues 90 - 94 (chain G) 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 ASP 90 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ILE* 2.8 14.2 - - + +
89G GLU* 1.3 79.1 - - + +
91G MET* 1.3 57.5 + - - +
92G ALA* 2.8 26.4 + - - +
93G MET* 2.8 38.0 + - + +
118G TYR* 3.2 6.3 - - + -
120G GLY 3.3 11.2 + - - +
148G ARG* 2.8 12.5 + - - +
716G LEU* 6.0 1.3 - - + -
764G MLY 2.2 44.4 - - - +
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Residues in contact with MET 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ILE* 3.5 4.2 - - - +
90G ASP* 1.3 71.1 - - - +
92G ALA* 1.3 56.0 + - - +
93G MET 2.9 6.4 + - - -
94G MET* 2.9 43.1 + - - +
97G LEU* 4.0 4.7 - - - +
102G VAL* 3.9 31.6 - - + +
105G ASN* 3.4 29.4 - - - +
106G LEU* 3.1 38.8 - - + -
117G THR* 3.5 9.4 - - - +
118G TYR 3.0 9.3 + - - +
119G SER* 3.4 33.9 - - - +
124G VAL* 4.3 6.1 - - + -
700G VAL* 5.8 0.7 - - + -
704G ILE* 5.8 1.8 - - + -
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ASP* 2.8 16.2 + - - +
91G MET* 1.3 78.2 - - - +
93G MET* 1.3 52.1 + - - +
94G MET 3.3 1.8 - - - -
97G LEU* 4.8 7.4 - - + -
119G SER* 4.3 3.5 + - - +
120G GLY* 3.9 21.4 - - - +
704G ILE* 4.8 9.2 - - + -
707G CYS* 4.7 6.1 - - + -
712G PRO 2.6 14.1 - - - +
714G ARG* 2.2 50.7 - - - +
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Residues in contact with MET 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G TYR* 3.9 13.9 + - + -
88G ILE* 4.7 11.4 - - + -
90G ASP* 2.8 21.3 + - + +
92G ALA* 1.3 77.8 - - - +
94G MET* 1.3 69.6 + - - +
95G THR 3.6 0.2 + - - -
713G SER* 3.0 11.8 - - - -
714G ARG* 0.9 59.3 + - + +
715G VAL* 4.2 4.4 + - - +
716G LEU* 3.1 35.0 - - + +
764G MLY 1.9 68.2 - - + +
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Residues in contact with MET 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ASN* 3.2 21.8 - - + +
85G TYR* 4.2 22.4 - - + +
88G ILE* 4.8 7.1 - - + +
90G ASP 4.1 0.2 + - - -
91G MET* 2.9 43.4 + - - +
93G MET* 1.3 78.2 - - - +
95G THR* 1.3 54.8 + - - +
96G HIS 3.1 13.0 + - - +
97G LEU* 3.7 12.8 - - + +
101G ALA* 3.0 50.9 - - + +
102G VAL* 4.4 4.0 - - + +
105G ASN* 4.8 9.0 - - + +
712G PRO 3.8 0.2 - - - -
713G SER* 2.4 31.5 + - - -
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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