Contacts of the helix formed by residues 680 - 687 (chain A) in PDB entry 3W3M
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 ASN 680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A ILE 6.1 0.2 - - - +
656A ASN* 2.8 21.2 + - - +
678A PHE* 4.0 11.1 - - + -
679A PHE* 1.3 85.8 - - - +
681A TRP* 1.3 65.9 + - - +
682A THR* 3.5 13.2 + - - -
683A LEU* 3.4 27.3 + - + +
684A LEU 4.4 0.5 + - - -
916A NAG 1.4 70.9 + - - +
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Residues in contact with TRP 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A PHE* 3.3 49.3 + + + +
680A ASN* 1.3 69.7 + - - +
682A THR* 1.3 61.0 + - - +
683A LEU 3.0 2.2 - - - -
684A LEU* 2.9 42.3 + - + +
693A LEU* 4.3 5.2 - - + -
695A LEU* 3.7 21.3 - - + -
700A LEU* 5.0 2.2 - - + -
702A PHE* 3.5 38.4 + + - -
703A LEU* 4.0 13.7 - - + -
704A THR* 3.5 39.8 - - + +
707A LEU* 4.1 13.5 - - + -
710A PHE* 3.6 15.5 - - + +
714A LEU* 5.8 0.2 - - + -
717A LEU* 4.3 24.9 - - + -
719A LEU* 4.2 15.7 - - + -
731A PHE* 5.9 1.6 - + - -
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Residues in contact with THR 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A ASN* 3.3 14.6 + - - -
681A TRP* 1.3 79.3 - - - +
683A LEU* 1.3 61.5 + - - +
684A LEU 3.1 0.4 - - - -
685A GLN* 3.2 42.1 + - - +
710A PHE* 3.3 38.4 - - + -
916A NAG 4.4 21.7 + - - +
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ILE 5.5 1.3 - - - +
656A ASN* 3.3 31.4 - - + +
659A PHE* 3.7 42.8 - - + -
660A LEU* 3.6 25.5 - - + +
680A ASN* 3.5 25.8 - - + +
681A TRP 3.0 0.4 - - - -
682A THR* 1.3 73.7 - - - +
684A LEU* 1.3 59.7 + - - +
685A GLN 3.0 6.6 + - - -
686A GLN* 3.2 15.4 + - - +
687A PHE* 3.5 14.6 - - - -
916A NAG 3.2 35.9 - - - +
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Residues in contact with LEU 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A PHE* 4.4 12.8 - - + -
679A PHE* 4.3 13.5 - - + -
681A TRP* 2.9 30.6 + - + +
683A LEU* 1.3 73.9 - - - +
685A GLN* 1.3 63.1 + - - +
686A GLN 3.0 3.1 - - - -
687A PHE* 3.0 26.1 + - + +
690A LEU* 3.9 26.0 - - + -
693A LEU* 4.0 25.1 - - + -
707A LEU* 4.0 25.4 - - + -
710A PHE* 3.5 12.5 - - + +
711A THR* 4.2 17.7 - - + -
714A LEU* 5.0 4.0 - - + -
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Residues in contact with GLN 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A THR* 3.2 28.9 + - - +
683A LEU 3.0 0.4 - - - -
684A LEU* 1.3 78.6 - - - +
686A GLN* 1.3 75.1 + - + +
687A PHE 3.2 0.9 + - - -
688A PRO* 4.7 6.8 - - - +
709A ASP* 4.2 9.3 + - - +
710A PHE* 3.2 47.8 + - - +
916A NAG 5.3 2.3 + - - -
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Residues in contact with GLN 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A LEU* 3.6 30.7 - - + +
664A ALA* 3.7 13.5 - - - +
683A LEU* 3.2 9.8 + - - +
684A LEU 3.0 1.6 - - - -
685A GLN* 1.3 93.0 + - + +
687A PHE* 1.3 76.5 + - + +
688A PRO* 3.3 10.9 - - - +
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Residues in contact with PHE 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A PHE* 3.2 55.0 - + - -
660A LEU* 4.6 4.7 - - - -
662A LEU* 3.5 24.0 - - + -
663A PRO 3.2 28.0 - - - -
664A ALA* 3.8 9.2 - - + -
666A LEU* 4.7 12.6 - - + +
669A LEU* 6.3 1.8 - - + -
683A LEU 3.5 15.7 - - - -
684A LEU* 3.0 19.9 + - + +
685A GLN 3.2 1.0 - - - -
686A GLN* 1.3 91.7 - - + +
688A PRO* 1.3 60.8 - - - +
689A ARG 3.2 3.4 + - - +
690A LEU* 3.5 29.7 + - + +
711A THR* 4.2 2.6 + - - -
713A SER* 3.2 14.4 + - - -
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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