Contacts of the helix formed by residues 698 - 708 (chain A) in PDB entry 3WOR
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 698 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A PHE* 3.9 20.5 - - - -
668A LEU* 5.2 2.0 - - - -
669A VAL* 2.9 26.9 + - - -
670A GLY* 4.4 3.6 - - - -
696A VAL 3.5 2.0 + - - -
697A ASP* 1.3 70.6 - - - +
699A ARG* 1.3 60.8 + - - +
701A LEU* 3.3 11.1 + - - +
702A ARG* 3.1 28.8 + - - +
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Residues in contact with ARG 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 3.6 21.6 - - - +
261A LEU* 2.9 34.7 + - - +
600A PHE* 3.9 4.8 - - - -
634A LEU* 3.5 36.9 + - + +
636A ASP* 2.9 33.3 + - - +
642A VAL* 4.1 5.7 - - + +
643A PRO* 3.4 23.9 - - + +
697A ASP* 2.8 45.0 + - - +
698A GLY* 1.3 74.1 - - - +
700A TYR* 1.3 59.9 + - - +
702A ARG* 3.4 12.5 + - - +
703A TRP* 2.8 29.3 + - - +
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Residues in contact with TYR 700 (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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206A VAL* 4.5 4.3 - - + +
221A HIS 4.4 3.2 + - - -
222A THR 4.2 0.2 - - - -
223A GLY* 3.6 35.6 + - - -
225A PHE* 5.5 0.2 - + - -
603A LEU* 3.5 33.2 - - + -
606A VAL* 4.0 13.0 - - + +
622A LEU* 3.5 22.7 - - - +
642A VAL* 4.6 1.1 - - + -
643A PRO 3.4 17.3 + - - +
644A VAL* 3.8 36.3 - - + +
696A VAL* 4.1 9.0 - - + -
697A ASP 2.9 9.8 + - - +
699A ARG* 1.3 78.0 - - - +
701A LEU* 1.3 66.3 + - - +
703A TRP* 3.8 17.3 - + + -
704A ILE* 2.9 42.0 + - + +
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Residues in contact with LEU 701 (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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82A VAL* 4.1 19.7 - - + -
225A PHE* 3.3 57.2 - - + -
227A PHE* 4.5 7.4 - - + -
256A PHE* 4.7 16.4 - - + -
668A LEU* 5.7 3.1 - - + -
671A LEU* 4.6 9.2 - - + -
696A VAL* 3.9 19.1 - - + +
697A ASP 3.2 13.7 + - - +
698A GLY* 3.4 11.2 - - - +
700A TYR* 1.3 75.9 - - - +
702A ARG* 1.3 65.1 + - + +
704A ILE* 3.4 1.9 + - - +
705A MET* 3.1 33.6 + - - +
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Residues in contact with ARG 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PHE* 3.8 32.2 - - + +
257A ALA 4.1 17.2 + - - -
634A LEU* 3.7 35.1 - - + +
698A GLY 3.1 18.6 + - - +
699A ARG* 3.8 10.6 - - - +
701A LEU* 1.3 79.1 - - - +
703A TRP* 1.3 63.6 + - - +
705A MET* 3.2 3.9 + - - +
706A GLN* 2.9 35.8 + - - +
715A LEU* 4.3 12.1 - - + +
720A VAL* 3.8 46.9 + - + +
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Residues in contact with TRP 703 (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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603A LEU* 3.6 35.9 - - + +
622A LEU* 4.0 9.4 - - + -
625A ALA* 3.7 24.0 - - + -
626A VAL* 3.8 23.8 - - + -
630A ARG 2.9 21.4 + - - -
631A TYR* 3.6 26.1 - - - +
632A GLY* 4.8 0.7 - - - -
634A LEU* 3.6 10.7 - - + +
642A VAL* 4.0 12.6 - - + -
699A ARG 2.8 19.3 + - - +
700A TYR* 3.3 16.8 + + - +
702A ARG* 1.3 74.3 - - - +
704A ILE* 1.3 74.2 + - + +
706A GLN* 3.1 3.1 + - - +
707A GLU* 2.8 43.6 + - + +
708A VAL* 3.6 24.9 - - + -
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Residues in contact with ILE 704 (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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200A TYR* 4.0 15.7 - - - +
202A PRO* 4.5 4.9 - - + -
206A VAL* 3.8 29.4 - - + -
225A PHE* 4.1 15.0 - - + -
622A LEU* 3.9 9.4 - - + -
700A TYR* 2.9 43.4 + - + +
701A LEU 3.8 3.6 - - - +
703A TRP* 1.3 99.6 - - + +
705A MET* 1.3 59.4 + - - +
708A VAL* 3.0 25.2 + - + -
709A TYR* 2.9 31.2 + - + +
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Residues in contact with MET 705 (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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200A TYR* 3.7 21.3 - - + +
225A PHE* 3.9 9.0 - - + -
227A PHE* 3.5 38.6 - - + -
256A PHE* 6.4 0.7 - - - -
701A LEU* 3.1 23.5 + - - +
702A ARG* 3.2 4.5 + - - +
704A ILE* 1.3 75.3 - - - +
706A GLN* 1.3 55.7 + - - +
709A TYR 3.8 8.5 - - - -
710A PRO* 3.2 6.0 - - - +
711A ALA* 3.0 34.0 + - + +
712A PRO* 4.5 0.9 - - - +
714A LEU* 3.8 30.5 - - + -
715A LEU* 3.6 32.3 - - + +
718A MET* 4.4 2.9 - - + -
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Residues in contact with GLN 706 (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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632A GLY* 3.0 34.1 + - - +
634A LEU* 3.8 22.0 - - - +
702A ARG* 2.9 29.6 + - - +
703A TRP* 3.7 3.3 - - - +
705A MET* 1.3 78.1 - - - +
707A GLU* 1.3 74.6 + - + +
708A VAL 3.7 0.7 - - - -
710A PRO* 3.9 15.5 - - - +
715A LEU* 3.5 20.0 - - + +
720A VAL 4.5 8.9 + - - -
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Residues in contact with GLU 707 (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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621A ALA* 4.2 13.7 - - - +
625A ALA* 4.2 10.3 - - + +
630A ARG* 2.9 52.5 + - - +
632A GLY* 4.2 14.2 - - - -
703A TRP* 2.8 51.8 + - + +
706A GLN* 1.3 88.8 - - + +
708A VAL* 1.3 60.9 + - + +
710A PRO* 4.9 3.3 - - - +
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Residues in contact with VAL 708 (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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203A PRO* 5.7 0.4 - - + -
206A VAL* 4.7 1.8 - - + -
619A PRO* 4.0 31.6 - - + +
621A ALA* 3.9 14.9 - - + +
622A LEU* 3.7 28.3 - - + +
703A TRP* 3.6 34.5 - - + -
704A ILE* 3.0 25.6 + - + +
706A GLN 3.7 0.6 - - - -
707A GLU* 1.3 83.8 - - + +
709A TYR* 1.3 66.5 + - + +
710A PRO* 3.7 7.5 - - - +
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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