Contacts of the helix formed by residues 639 - 644 (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 GLY 639 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541G MET* 5.3 0.2 - - - -
632G GLY 3.1 0.7 - - - +
633G GLY* 4.0 4.4 - - - -
638G GLY* 1.3 63.4 - - - -
640G LYS* 1.3 55.6 + - - -
641G LYS 3.1 3.4 - - - -
23V GLY 2.4 26.5 - - - +
24V ASP 2.8 6.8 + - - +
341V ILE* 4.9 0.8 - - - +
344V SER* 2.4 38.2 + - - -
345V ILE* 1.9 19.0 - - - +
348V SER* 3.0 5.2 - - - -
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Residues in contact with LYS 640 (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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540G CYS 6.1 0.4 - - - -
600G MLY 3.2 38.0 + - - +
601G ASP 5.0 2.0 + - - -
602G PRO* 5.5 2.4 - - - +
629G GLU 4.1 0.9 - - - +
633G GLY* 4.8 7.0 - - - -
638G GLY 5.8 0.9 - - - +
639G GLY* 1.3 67.1 - - - -
641G LYS* 1.4 52.0 + - - +
643G GLY* 3.4 3.1 + - - -
645G SER* 2.1 60.6 + - - +
646G PHE 2.9 22.2 + - - +
647G GLN* 4.1 8.9 + - + +
23V GLY 2.1 24.5 - - - +
345V ILE* 6.0 0.9 - - + -
348V SER* 3.6 3.0 + - - -
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Residues in contact with LYS 641 (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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537G GLU* 5.1 1.8 + - - -
640G LYS* 1.4 70.1 - - - +
642G LYS* 1.2 52.0 + - - -
643G GLY 3.0 3.6 - - - -
644G SER* 2.9 20.7 + - - +
645G SER 3.2 12.1 - - - +
647G GLN* 1.8 76.9 - - + +
651G ALA* 5.0 10.0 - - - +
4V GLU* 3.3 54.4 - - + +
5V THR* 5.0 7.1 - - - +
21V PHE* 5.1 0.3 - - - +
22V ALA 2.6 12.3 - - - +
23V GLY* 1.6 14.4 - - - -
347V ALA 4.7 1.2 + - - -
348V SER* 1.8 32.0 + - - +
349V LEU 4.0 8.5 + - - -
350V SER* 4.3 3.4 - - - +
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Residues in contact with LYS 642 (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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641G LYS 1.2 35.1 - - - -
643G GLY* 1.3 46.2 - - - -
9V VAL* 4.3 0.7 - - - -
21V PHE* 2.2 30.1 - - - +
22V ALA* 2.7 6.7 - - - +
23V GLY* 1.0 103.5 - - - +
24V ASP* 1.0 190.4 - - + +
28V ARG* 3.5 4.2 + - - -
340V TRP* 2.5 49.7 + - + -
341V ILE* 2.9 8.5 + - - +
344V SER* 0.7 205.8 - - - +
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Residues in contact with GLY 643 (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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628G GLY 3.0 5.3 - - - +
629G GLU* 1.9 41.8 + - - -
631G GLU* 4.8 1.8 - - - -
632G GLY* 3.4 3.6 - - - -
642G LYS* 1.3 65.2 - - - +
644G SER* 1.3 74.0 + - - +
23V GLY 2.5 5.7 - - - -
24V ASP* 2.2 22.7 - - - +
28V ARG* 5.2 0.7 - - - -
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Residues in contact with SER 644 (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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625G THR 4.0 0.7 + - - -
628G GLY 3.5 2.6 + - - -
629G GLU* 0.7 139.0 + - - +
641G LYS* 2.9 15.0 + - - +
643G GLY* 1.3 81.0 + - - +
645G SER* 1.3 54.6 - - - +
646G PHE* 4.0 1.0 + - - -
4V GLU* 5.0 9.6 - - - +
5V THR* 6.1 4.0 - - - -
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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