Contacts of the helix formed by residues 626 - 632 (chain T) in PDB entry 2P8W
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 626 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620T ALA* 4.3 0.2 - - - -
624T GLY 3.9 0.8 + - - -
625T TRP* 1.3 75.4 - - - +
627T VAL* 1.3 67.4 + - - +
628T THR* 3.0 29.9 + - - -
629T ASP* 3.0 32.4 + - - +
630T ALA* 3.0 19.6 + - - +
685T ARG* 5.9 0.8 - - - +
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Residues in contact with VAL 627 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613T LYS 5.7 0.2 - - - +
616T ALA* 3.8 26.5 - - + +
617T ARG* 3.8 34.1 - - + +
620T ALA* 3.7 14.3 - - + +
625T TRP 3.5 4.6 + - - -
626T ASP* 1.3 74.8 + - - +
628T THR* 1.3 67.1 + - - +
630T ALA* 4.3 3.4 - - - -
631T ARG* 2.9 48.0 + - + +
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Residues in contact with THR 628 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626T ASP* 3.0 13.1 + - - -
627T VAL* 1.3 82.4 - - - +
629T ASP* 1.3 69.5 + - - +
631T ARG* 3.3 8.6 + - + +
632T LYS* 3.0 47.3 + - + +
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Residues in contact with ASP 629 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625T TRP* 4.1 9.6 - - + -
626T ASP* 3.0 33.4 + - + +
628T THR* 1.3 79.1 - - - +
630T ALA* 1.3 64.6 + - - +
632T LYS* 3.1 14.9 + - - +
633T ILE 3.4 7.4 + - - -
647T ILE* 3.5 16.6 - - + +
648T ASP 5.2 0.9 - - - +
649T GLN* 2.8 28.6 + - - +
685T ARG* 2.8 33.5 + - - +
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Residues in contact with ALA 630 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612T PHE 4.9 1.4 - - - +
615T ARG* 4.9 3.1 + - - -
616T ALA* 3.6 33.4 - - + +
619T MET* 4.0 21.8 - - + +
625T TRP* 3.9 11.4 - - + -
626T ASP 3.0 15.0 + - - +
627T VAL* 3.8 1.6 - - - +
629T ASP* 1.3 73.3 - - - +
631T ARG* 1.3 59.8 + - - +
632T LYS 2.9 4.7 - - - -
633T ILE* 2.8 31.6 - - - +
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Residues in contact with ARG 631 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612T PHE* 3.4 58.7 - - + +
613T LYS* 4.9 18.3 - - - +
615T ARG* 5.7 0.2 + - - -
616T ALA* 3.4 19.7 - - + -
627T VAL* 2.9 42.4 + - - +
628T THR* 3.8 9.0 - - - +
630T ALA* 1.3 75.0 - - - +
632T LYS* 1.3 62.4 + - + +
633T ILE 3.5 3.3 + - - +
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Residues in contact with LYS 632 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628T THR* 3.0 34.9 + - + +
629T ASP* 3.4 8.5 - - - +
630T ALA 2.9 1.4 - - - -
631T ARG* 1.3 84.0 - - + +
633T ILE* 1.3 65.2 + - - +
634T TRP* 3.2 10.8 + - + +
647T ILE* 4.5 0.4 - - + -
648T ASP* 3.2 61.1 + - + +
649T GLN* 5.3 1.2 - - - +
650T THR 4.2 13.5 + - - -
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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