Contacts of the helix formed by residues 688 - 692 (chain A) in PDB entry 4D2Y
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 THR 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU* 5.0 0.7 - - - -
651A HIS* 4.0 20.2 - - + +
652A HIS* 3.9 19.7 - - + +
655A THR* 3.5 22.0 - - - +
681A PRO* 3.8 11.5 - - + +
684A SER 3.7 11.9 - - - +
685A GLY 2.7 20.3 + - - +
686A SER 4.5 0.2 - - - -
687A ILE* 1.3 83.4 - - - +
689A PRO* 1.3 69.6 - - - +
690A VAL* 3.3 15.9 + - - +
691A PHE* 3.3 12.0 + - - +
692A HIS* 3.7 7.3 - - - -
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Residues in contact with PRO 689 (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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305A ASN* 3.9 13.8 + - - +
307A GLU* 3.9 17.7 - - - +
652A HIS* 4.9 4.0 - - + +
655A THR* 3.5 8.7 - - - +
656A GLU* 3.9 24.7 - - + +
659A ILE* 3.7 26.0 - - + -
687A ILE 4.5 2.0 - - - +
688A THR* 1.3 87.2 - - - +
690A VAL* 1.3 62.6 + - - +
692A HIS* 3.2 13.7 + - - +
693A GLN 3.6 5.5 + - - -
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Residues in contact with VAL 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A THR* 3.7 37.2 - - + +
658A PHE* 4.0 8.7 - - + -
659A ILE* 3.7 19.1 - - + -
676A TRP* 3.3 12.1 + - - -
679A ILE* 3.9 17.9 - - + +
680A VAL* 4.0 11.4 - - + -
681A PRO* 3.9 11.2 - - + -
688A THR* 3.5 16.4 - - - +
689A PRO* 1.3 74.6 - - - +
691A PHE* 1.3 67.4 + - - +
693A GLN* 3.1 21.2 + - - +
695A MET* 3.6 12.6 - - + +
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Residues in contact with PHE 691 (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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676A TRP* 3.2 46.3 + + - -
680A VAL* 4.0 7.0 - - + -
685A GLY* 3.2 24.5 - - - +
686A SER* 3.4 27.8 - - - -
688A THR 3.3 7.0 + - - +
689A PRO 3.1 0.6 - - - -
690A VAL* 1.3 81.4 - - - +
692A HIS* 1.3 64.3 + + + +
693A GLN 3.4 1.0 + - - -
596B ARG* 3.7 24.2 - - - -
677B VAL 5.0 1.3 - - - -
680B VAL 5.3 4.0 - - - -
681B PRO 5.4 0.4 - - - -
682B PRO* 4.1 28.7 - - + -
760B H4B 2.7 59.2 + + - -
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Residues in contact with HIS 692 (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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304A LYS 3.8 0.7 - - - +
305A ASN* 3.3 3.9 - - - +
306A TRP* 2.8 37.4 + - + +
307A GLU* 3.4 52.0 + - + +
686A SER 2.8 27.5 + - - -
688A THR 3.7 10.3 - - - -
689A PRO 3.2 5.7 + - - +
690A VAL 3.1 0.4 - - - -
691A PHE* 1.3 87.3 - + + +
693A GLN* 1.3 59.3 + - - +
694A GLU 3.8 1.0 + - - -
596B ARG* 3.7 20.0 + - - -
600B ASP* 3.4 29.9 + - - -
601B ASN 5.9 0.8 + - - -
602B SER* 5.8 1.5 + - - -
760B H4B 3.6 10.8 + - - -
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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