Contacts of the helix formed by residues 689 - 693 (chain A) in PDB entry 5UO5
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 SER 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636A VAL* 5.6 0.2 - - - +
656A HIS* 4.2 4.9 - - - -
688A MET* 1.3 83.5 - - - +
690A GLY* 1.3 66.3 + - - +
691A SER 3.4 2.5 - - - -
692A ILE* 3.1 34.1 + - - +
693A THR* 3.8 6.1 + - - +
632B ASP* 2.7 35.2 + - - +
635B LEU* 4.6 5.5 - - - +
687B PRO 3.7 1.8 - - - -
688B MET* 4.1 13.1 - - - +
689B SER 3.5 11.3 - - - +
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Residues in contact with GLY 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 3.9 22.8 - - - +
686A PRO* 4.3 3.8 + - - -
688A MET 3.1 6.4 + - - -
689A SER* 1.3 73.8 - - - +
691A SER* 1.3 62.0 + - - +
693A THR* 2.8 26.8 + - - -
696A PHE* 3.2 15.8 - - - +
686B PRO 5.7 0.7 - - - -
687B PRO 3.2 10.9 + - - -
688B MET* 4.2 0.4 - - - +
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Residues in contact with SER 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 5.1 1.2 - - - +
690A GLY* 1.3 73.8 - - - +
692A ILE* 1.3 61.7 + - - +
693A THR 3.2 3.9 + - - +
696A PHE* 3.4 27.4 - - - -
697A HIS* 3.1 20.5 + - - -
600B VAL* 2.9 31.5 - - - +
601B ARG* 3.7 14.0 - - - -
605B ASP* 4.4 7.4 + - - +
687B PRO* 3.0 20.3 + - - -
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Residues in contact with ILE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A HIS* 3.9 29.3 + - + -
689A SER* 3.1 35.6 + - - +
691A SER* 1.3 83.7 - - - +
693A THR* 1.3 57.2 + - - +
694A PRO* 4.8 0.7 - - - +
600B VAL* 5.0 0.2 - - + -
604B CYS* 4.5 15.0 - - + +
612B LEU* 4.1 19.7 - - + -
631B LYS* 4.0 38.1 + - + +
632B ASP 4.2 0.9 - - - +
635B LEU* 4.1 28.9 - - + -
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Residues in contact with THR 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 5.4 0.4 - - - -
656A HIS* 4.1 25.4 - - + +
657A HIS* 4.2 9.0 - - + +
660A THR* 3.5 22.0 - - - +
686A PRO* 3.8 15.8 - - + +
689A SER 3.8 11.7 - - - +
690A GLY 2.8 17.3 + - - +
691A SER 3.8 4.7 - - - +
692A ILE* 1.3 83.3 - - - +
694A PRO* 1.3 69.0 - - - +
695A VAL* 3.3 18.2 + - - +
696A PHE* 3.4 11.8 + - - +
697A HIS* 4.1 3.3 - - - -
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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
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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