Contacts of the helix formed by residues 665 - 669 (chain A) in PDB entry 3HOU
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 665 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664A THR* 1.3 75.1 + - - +
666A ILE* 1.3 54.5 + - - -
667A GLY* 3.0 3.8 - - - -
668A ASP* 2.6 41.5 + - - +
669A THR* 4.0 1.4 + - - +
1026B LEU* 3.8 14.8 - - - +
1069B PHE* 3.9 9.4 - - - -
1086B PHE* 3.9 18.4 - - - -
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A GLY* 1.3 69.1 - - - -
667A GLY* 1.3 63.0 + - - +
669A THR* 2.5 42.1 + - - +
670A ILE* 2.9 8.9 - - - +
805A LEU* 4.4 3.1 - - + -
1023B VAL* 3.8 21.3 - - + -
1026B LEU* 3.4 43.2 - - + +
1027B ILE* 3.9 12.3 - - + -
1030B LEU* 4.1 16.6 - - + -
1052B VAL* 4.2 19.3 - - + -
1067B ARG* 2.8 37.0 - - + +
1086B PHE* 3.6 8.1 - - + -
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Residues in contact with GLY 667 (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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665A GLY 2.8 2.2 + - - -
666A ILE* 1.3 86.8 - - - +
668A ASP* 1.3 57.1 + - - +
669A THR 3.2 0.2 - - - -
670A ILE* 3.2 27.6 + - - +
1067B ARG* 3.9 13.9 - - - -
1069B PHE* 4.0 3.3 - - - -
192C TRP* 2.8 37.1 - - - -
194C GLU* 5.0 1.0 - - - +
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Residues in contact with ASP 668 (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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664A THR* 3.4 4.9 - - - +
665A GLY 2.6 35.5 + - - +
667A GLY* 1.3 71.0 - - - -
669A THR* 1.3 59.3 + - - +
670A ILE 3.7 1.1 - - - -
737A LEU* 4.3 8.5 - - - +
741A ASN* 2.8 28.6 + - - +
742A ASN* 2.7 54.5 + - - -
743A VAL* 3.7 22.4 - - + +
762A SER* 5.2 0.2 + - - -
1069B PHE* 3.6 4.0 - - - -
192C TRP* 3.2 14.0 + - - -
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Residues in contact with THR 669 (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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665A GLY 5.0 0.9 - - - +
666A ILE* 2.5 35.9 + - - +
668A ASP* 1.3 76.5 - - - +
670A ILE* 1.3 57.8 + - - +
676A MET* 5.0 0.2 - - - +
737A LEU* 5.9 1.3 - - - -
743A VAL* 4.8 5.2 - - + -
761A MET* 3.5 45.3 - - + -
762A SER* 2.9 35.7 - - - +
805A LEU* 3.0 26.5 - - - +
1017B ILE* 6.3 0.4 - - + -
1023B VAL* 4.7 4.1 - - + +
1026B LEU* 4.7 13.2 - - + -
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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