Contacts of the helix formed by residues 695 - 706 (chain C) in PDB entry 2W4T
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 695 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488C PHE* 4.5 1.3 - - - -
492C MET* 4.4 5.9 - - - +
514C MET* 4.0 25.3 - - - +
691C LEU 4.6 0.2 - - - -
692C GLN 3.4 10.8 + - - -
693C CYS 3.5 1.2 - - - -
694C ASN* 1.3 84.9 - - - +
696C VAL* 1.3 52.0 - - - -
697C LEU 3.6 1.6 - - - -
698C GLU* 3.6 6.3 + - - +
699C GLY* 2.7 34.1 + - - -
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Residues in contact with VAL 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLU* 4.0 6.1 - - - +
99C VAL* 5.0 6.5 - - + -
116C SER* 5.7 7.0 - - - -
488C PHE* 6.4 0.2 - - - -
669C ARG* 3.3 18.4 - - - +
691C LEU* 2.5 56.3 - - + +
694C ASN* 2.2 34.5 - - - +
695C GLY* 1.3 74.1 - - - +
697C LEU* 1.3 80.3 + - + +
699C GLY* 2.7 13.5 + - - -
700C ILE* 3.0 19.3 + - + +
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Residues in contact with LEU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU* 2.7 33.4 - - + +
95C ASN* 4.0 10.1 - - + -
96C GLU* 4.5 15.7 - - + +
99C VAL* 5.0 8.1 - - + -
695C GLY 3.6 0.2 - - - -
696C VAL* 1.3 86.2 - - + +
698C GLU* 1.3 79.8 + - + +
700C ILE* 2.6 30.6 + - - +
701C ARG* 2.9 22.4 + - + +
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Residues in contact with GLU 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C PHE* 3.1 24.5 - - + -
512C PHE* 2.9 44.6 - - - +
514C MET* 4.6 9.9 - - + -
695C GLY* 3.6 8.4 + - - +
696C VAL 3.3 0.4 - - - -
697C LEU* 1.3 100.6 - - + +
699C GLY* 1.3 55.7 + - - +
700C ILE 2.7 15.8 + - - -
701C ARG* 2.9 35.5 + - - +
702C ILE* 3.2 13.7 + - - +
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Residues in contact with GLY 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C SER 4.3 4.9 - - - +
118C LEU* 5.3 1.6 + - - +
119C PHE* 5.7 3.6 - - - -
488C PHE* 4.8 2.5 - - - -
492C MET* 3.3 26.7 - - - +
493C PHE* 3.7 0.4 - - - -
695C GLY 2.7 17.8 + - - -
696C VAL* 2.7 8.5 + - - -
698C GLU* 1.3 74.7 - - - +
700C ILE* 1.3 63.0 + - - +
702C ILE* 2.9 16.9 - - - +
703C CYS* 4.4 4.5 - - - +
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Residues in contact with ILE 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C MET* 4.1 2.7 - - + -
89C ALA* 3.2 14.8 - - - +
94C LEU* 2.3 44.6 - - + -
99C VAL* 5.9 1.3 - - + -
116C SER* 2.7 59.7 - - - +
696C VAL* 3.0 19.3 - - + +
697C LEU* 2.6 14.9 + - - +
698C GLU 2.7 0.2 + - - -
699C GLY* 1.3 74.1 - - - +
701C ARG* 1.3 61.3 + - - -
702C ILE 3.3 2.0 - - - -
703C CYS* 2.2 42.4 - - - -
704C ARG* 3.1 3.6 + - - +
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Residues in contact with ARG 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LEU* 4.4 0.8 - - + +
512C PHE* 4.4 12.6 - - + -
697C LEU* 2.9 17.1 + - + +
698C GLU* 2.9 35.1 + - - +
700C ILE* 1.3 74.1 - - - +
702C ILE* 1.3 49.9 + - - +
704C ARG* 2.9 11.3 + - - +
705C LYS* 2.3 87.1 + - + +
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Residues in contact with ILE 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492C MET* 4.2 21.8 - - + +
493C PHE* 3.3 11.9 - - + -
496C GLU* 4.7 16.2 - - + +
507C TRP* 6.4 0.4 - - + -
510C ILE* 6.0 0.7 - - + -
512C PHE* 3.1 39.3 - - + -
698C GLU 3.2 11.7 - - - +
699C GLY* 2.9 34.1 - - - +
701C ARG* 1.3 74.0 - - - +
703C CYS* 1.3 62.4 + - + +
705C LYS* 3.8 9.4 - - - -
706C GLY* 2.8 31.4 + - - +
708C PRO* 5.7 0.3 - - - +
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Residues in contact with CYS 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.0 37.7 - - + -
117C GLY* 4.0 15.3 - - - -
118C LEU* 4.8 7.4 - - + +
699C GLY 4.4 4.0 - - - +
700C ILE* 2.2 44.0 + - - -
702C ILE* 1.3 85.3 - - + +
704C ARG* 1.3 59.5 + - - +
706C GLY 4.7 0.9 + - - -
708C PRO* 4.9 12.6 - - - +
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Residues in contact with ARG 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.8 21.4 + - - +
91C MET 2.8 32.1 + - - -
92C THR* 3.3 18.1 + - - +
94C LEU* 3.8 35.8 - - - +
700C ILE* 3.1 7.3 + - + +
701C ARG* 2.9 8.9 + - - +
703C CYS* 1.3 79.8 - - - +
705C LYS* 1.3 95.6 + - + +
706C GLY 3.6 2.1 + - - +
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Residues in contact with LYS 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C TRP* 4.2 12.2 - - + -
510C ILE* 6.4 2.2 - - + -
512C PHE* 5.9 4.0 - - + -
701C ARG* 2.3 89.4 + - + +
702C ILE* 3.8 6.1 - - + -
704C ARG* 1.3 105.1 - - + +
706C GLY* 1.2 66.9 + - - +
707C PHE* 5.1 0.3 - - - -
763C LYS* 4.3 14.0 + - - -
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Residues in contact with GLY 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C TYR* 4.3 3.8 - - - -
507C TRP* 3.1 19.1 - - - -
702C ILE* 2.8 23.5 + - - -
703C CYS 4.6 0.6 - - - -
704C ARG 3.5 3.1 - - - +
705C LYS* 1.2 80.2 - - - +
707C PHE* 1.3 67.8 + - - -
708C PRO* 3.1 13.5 - - - +
763C LYS* 4.9 5.9 - - - +
764C ALA* 4.9 3.1 + - - +
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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