Contacts of the strand formed by residues 953 - 957 (chain M) 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 ASN 953 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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880M LYS* 4.1 28.8 - - + -
881M GLN 3.5 3.7 - - - +
882M SER* 3.2 30.0 + - - -
951M GLU* 3.4 22.0 + - - +
952M ALA* 1.3 79.5 - - - +
954M TRP* 1.3 75.7 + - - +
955M PRO* 4.6 0.2 - - - +
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Residues in contact with TRP 954 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880M LYS* 3.8 2.8 - - - +
881M GLN 2.8 33.6 + - - +
883M LEU* 4.6 5.4 - - + -
947M PHE* 3.3 55.3 - + + -
949M ASP* 6.1 0.7 - - + -
951M GLU* 2.7 45.3 + - + -
952M ALA 3.5 11.9 - - - -
953M ASN* 1.3 83.8 + - - +
955M PRO* 1.3 81.4 - - + +
956M LEU* 3.3 17.1 + - + +
1017M LEU* 5.4 0.9 - - + -
203Q GLU* 3.7 43.3 - - + +
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Residues in contact with PRO 955 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517M ASN* 4.0 13.7 - - - +
878M ILE* 3.3 25.2 - - + +
879M GLU 3.0 14.1 - - - +
880M LYS* 3.8 17.2 - - + +
953M ASN 4.6 0.7 - - - +
954M TRP* 1.3 98.1 - - + +
956M LEU* 1.3 65.9 + - - +
1362M TYR* 3.9 16.8 - - + +
1364M ASN* 4.7 4.7 - - - +
1365M TYR* 6.5 1.1 - - + -
203Q GLU* 4.9 12.8 - - - +
204Q THR* 5.1 5.1 + - - +
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Residues in contact with LEU 956 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878M ILE* 3.5 7.7 - - - +
879M GLU* 2.7 21.4 + - - +
881M GLN* 3.1 24.0 + - + +
883M LEU* 3.9 28.5 - - + -
954M TRP* 3.3 24.8 + - + +
955M PRO* 1.3 77.7 - - - +
957M PRO* 1.3 80.3 - - + +
958M VAL 4.5 0.2 - - - -
1017M LEU* 3.6 35.0 - - + +
1018M PHE* 4.3 18.6 - - + +
1021M LEU* 4.1 12.6 - - + -
204Q THR 4.2 7.9 - - - +
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Residues in contact with PRO 957 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871M ASP* 4.5 7.2 - - - +
873M MET* 3.4 48.9 - - + -
877M HIS 3.5 12.1 - - - +
878M ILE* 4.0 5.9 - - + -
881M GLN* 3.0 3.8 + - - -
956M LEU* 1.3 98.4 - - + +
958M VAL* 1.3 75.9 + - + +
1018M PHE* 3.3 25.9 - - + -
1053M PHE* 4.4 6.5 - - + -
1056M SER* 3.8 14.1 - - - -
204Q THR 5.9 0.2 - - - +
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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