Contacts of the helix formed by residues 693 - 697 (chain A) in PDB entry 4UH6
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 693 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 5.5 0.4 - - - -
656A HIS* 4.2 18.4 - - + +
657A HIS* 4.3 9.0 - - + +
660A THR* 3.5 21.1 - - - +
686A PRO* 3.8 21.5 - - + +
689A SER 3.7 14.8 - - - +
690A GLY 2.6 19.5 + - - +
692A ILE* 1.3 83.2 - - - +
694A PRO* 1.3 69.0 - - - +
695A VAL* 3.3 18.0 + - - +
696A PHE* 3.4 11.3 + - - +
697A HIS* 3.8 8.1 - - - -
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Residues in contact with PRO 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 4.0 13.2 + - - +
312A GLU* 4.3 19.0 - - - +
657A HIS* 4.8 4.0 - - - +
660A THR* 3.3 18.8 - - - +
661A GLU* 3.8 33.2 - - + +
664A ILE* 3.9 14.3 - - + +
692A ILE 4.5 2.2 - - - +
693A THR* 1.3 83.5 - - - +
695A VAL* 1.3 61.8 + - - +
697A HIS* 3.3 12.3 + - + +
698A GLN* 3.7 6.6 + - - +
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Residues in contact with VAL 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A THR* 3.6 41.5 - - + +
663A PHE* 3.9 14.6 - - + -
664A ILE* 4.0 8.1 - - + -
681A TRP* 3.3 12.0 + - - -
684A ILE* 3.8 18.6 - - + -
685A VAL* 3.9 12.8 - - + -
686A PRO* 3.9 11.7 - - + -
693A THR* 3.4 18.2 - - - +
694A PRO* 1.3 75.0 - - - +
696A PHE* 1.3 65.9 + - - +
698A GLN* 3.1 19.9 + - - +
700A MET* 3.7 13.0 - - + +
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Residues in contact with PHE 696 (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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681A TRP* 3.1 47.5 + + - -
685A VAL* 4.1 6.1 - - + -
690A GLY* 3.3 24.5 - - - +
691A SER* 3.4 33.7 - - - -
693A THR 3.4 5.4 + - - +
694A PRO 3.2 0.4 - - - -
695A VAL* 1.3 80.1 - - - +
697A HIS* 1.3 63.9 + + + +
601B ARG* 3.5 30.7 - - - -
682B VAL 5.0 1.1 - - - -
685B VAL 5.2 4.5 - - - -
686B PRO 5.3 0.7 - - - -
687B PRO* 4.2 18.8 - - + -
760B H4B 2.6 60.7 + + - +
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Residues in contact with HIS 697 (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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309A LYS 3.9 0.3 - - - +
310A ASN* 3.5 4.5 - - - +
311A TRP* 2.9 34.8 + - + +
312A GLU* 3.9 49.5 + - + +
691A SER 2.8 27.8 + - - -
693A THR 3.8 12.6 - - - -
694A PRO 3.3 5.7 + - - +
695A VAL 3.1 0.6 - - - -
696A PHE* 1.3 87.8 - + + +
698A GLN* 1.3 59.9 + - - +
699A GLU 3.6 1.6 + - - -
601B ARG* 3.5 29.3 + - - -
605B ASP* 3.6 18.0 + - + -
607B SER* 6.0 0.9 - - - -
760B H4B 3.4 14.3 + - - +
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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
------------------------------------------------------------
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