Contacts of the strand formed by residues 956 - 961 (chain A) in PDB entry 4D86
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 GLU 956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A VAL* 3.5 15.9 - - + -
805A ILE* 4.4 6.3 - - + -
815A PRO 4.5 5.2 - - - +
914A ARG* 3.1 23.0 + - - +
915A SER* 3.2 20.5 - - - -
916A ILE* 3.1 23.6 + - - +
954A LEU* 4.5 1.0 - - - +
955A LYS* 1.3 87.0 - - + +
957A ILE* 1.3 64.5 + - - +
958A TYR* 3.5 32.1 + - + -
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Residues in contact with ILE 957 (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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798A LEU* 4.5 6.7 - - + -
802A VAL* 4.6 5.6 - - + -
803A VAL 2.9 10.3 + - - +
804A LEU* 3.3 20.6 - - + +
805A ILE* 2.7 32.4 + - - +
905A LEU* 5.1 4.0 - - + -
916A ILE* 3.6 22.7 - - + -
918A ILE* 4.1 17.9 - - + -
941A ILE* 3.9 18.4 - - + -
945A PHE* 3.1 43.1 - - + -
954A LEU* 4.7 9.9 - - + -
956A GLU* 1.3 79.4 - - - +
958A TYR* 1.3 63.0 + - - +
959A LEU* 4.6 0.4 - - + -
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Residues in contact with TYR 958 (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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795A ARG* 4.6 6.2 + - - -
805A ILE* 3.2 36.5 - - + +
807A GLN* 3.5 37.5 - - + -
814A LEU* 5.5 4.3 - - + -
815A PRO* 4.2 21.3 + - + +
816A VAL* 3.3 31.2 - - + -
916A ILE 2.8 13.1 + - - +
917A ALA* 3.3 6.7 - - + -
918A ILE* 2.8 28.8 + - - +
956A GLU* 3.5 31.5 + - + -
957A ILE* 1.3 76.9 - - - +
959A LEU* 1.3 63.4 + - - +
960A VAL* 3.9 14.1 - - + -
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Residues in contact with LEU 959 (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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804A LEU* 3.8 25.8 - - + -
805A ILE 2.8 10.6 + - - +
806A VAL* 3.4 20.5 - - + +
807A GLN 3.0 25.1 + - - +
918A ILE* 3.4 22.4 - - + +
937A ILE* 4.2 4.0 - - + -
938A VAL* 3.8 20.0 - - + -
941A ILE* 3.8 21.1 - - + -
957A ILE* 4.6 0.9 - - + -
958A TYR* 1.3 78.8 - - - +
960A VAL* 1.3 61.1 + - - +
967A VAL* 5.3 0.2 - - - +
970A PHE* 3.7 41.6 - - + -
974A VAL* 4.3 1.3 - - + -
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Residues in contact with VAL 960 (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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807A GLN* 3.2 23.3 - - + +
809A GLY* 3.3 31.2 - - - +
811A LEU* 4.9 7.9 - - + +
814A LEU* 3.9 27.8 - - + -
917A ALA* 4.5 2.9 - - + -
918A ILE 3.1 9.9 + - - +
919A PRO* 3.4 24.6 - - - +
920A ALA 4.2 0.5 + - - -
958A TYR* 3.9 23.6 - - + +
959A LEU* 1.3 81.9 - - - +
961A ASP* 1.3 68.3 + - - +
967A VAL* 4.8 0.7 - - - -
970A PHE* 3.9 8.8 - - - -
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Residues in contact with ASP 961 (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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807A GLN 3.7 2.6 + - - -
808A GLN* 3.4 8.7 - - - +
809A GLY 3.0 23.4 + - - -
833A LEU* 5.8 0.9 - - - +
919A PRO* 5.5 1.2 - - - +
920A ALA* 4.9 2.4 + - - +
960A VAL* 1.3 78.1 - - - +
962A VAL* 1.3 68.2 + - - +
963A SER* 2.8 37.0 + - - +
966A THR* 3.5 29.7 + - + +
967A VAL* 3.6 7.2 - - + +
1201A ADP 2.6 42.4 + - - +
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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