Contacts of the strand formed by residues 952 - 961 (chain B) in PDB entry 5J67
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 VAL 952 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B GLU* 5.8 0.7 - - - +
859B TYR* 3.2 4.7 - - - -
860B GLY 2.8 34.3 + - - +
929B LYS* 4.4 11.4 - - + -
930B GLY* 3.4 33.9 - - - +
950B THR* 3.9 6.7 - - - +
951B PRO* 1.3 76.3 - - - +
953B LEU* 1.3 77.6 + - + +
954B LEU* 3.3 2.5 + - + +
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Residues in contact with LEU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B GLU* 3.8 26.0 + - + +
737B VAL* 3.8 30.1 - - + -
854B ILE* 4.8 2.5 - - + -
857B ALA* 3.8 18.2 - - + -
858B LEU 3.9 2.9 - - - +
859B TYR* 3.3 29.1 - - + +
929B LYS* 4.4 8.8 + - - +
952B VAL* 1.3 83.8 - - + +
954B LEU* 1.3 65.8 + - - +
955B GLU 3.6 26.5 - - - +
956B ILE* 4.2 14.4 - - + -
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Residues in contact with LEU 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B ARG* 4.3 24.4 + - - +
812B LEU* 3.5 32.5 - - + -
858B LEU* 2.9 18.8 + - + +
859B TYR 3.8 2.0 - - - -
860B GLY* 3.7 22.4 - - - +
861B SER 4.2 1.1 - - - +
862B GLU* 4.0 30.7 - - + +
929B LYS* 4.1 30.5 + - + +
952B VAL 3.5 15.9 - - - +
953B LEU* 1.3 79.4 - - - +
955B GLU* 1.3 63.0 + - + +
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Residues in contact with GLU 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807B ARG* 5.3 1.2 + - - -
809B ARG* 3.6 34.1 + - - +
814B ARG* 4.9 2.6 + - - -
857B ALA* 3.4 6.4 - - - +
858B LEU* 2.9 51.7 + - + +
953B LEU* 3.6 2.2 - - - +
954B LEU* 1.3 80.5 - - - +
956B ILE* 1.3 63.5 + - - +
957B ASN* 3.6 22.3 + - - +
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Residues in contact with ILE 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B TYR* 3.5 37.5 - - + +
737B VAL* 4.0 9.2 - - + -
854B ILE* 3.7 38.6 - - + -
856B GLU 4.1 2.2 - - - -
857B ALA* 4.5 0.7 - - - -
953B LEU* 4.2 14.8 - - + -
955B GLU* 1.3 74.0 - - - +
957B ASN* 1.3 62.4 + - - +
958B ARG 4.0 2.9 - - - +
959B VAL* 3.5 30.3 - - + -
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Residues in contact with ASN 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B ARG* 3.3 32.3 + - - +
856B GLU* 2.9 29.0 + - - +
857B ALA* 3.4 18.3 - - - -
858B LEU* 3.4 1.8 + - - +
955B GLU* 3.6 33.5 + - - +
956B ILE* 1.3 73.4 - - - +
958B ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B LYS* 6.0 3.0 - - - +
854B ILE* 3.8 2.1 - - - +
855B ALA* 2.9 45.3 + - + +
856B GLU* 3.1 36.7 + - + +
956B ILE* 4.0 0.6 - - - +
957B ASN* 1.3 83.0 - - - +
959B VAL* 1.3 68.3 + - - +
960B VAL* 3.8 24.0 - - - +
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Residues in contact with VAL 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730B TYR* 3.6 26.7 - - + -
732B ASN* 4.3 11.4 - - - +
852B HIS* 3.8 26.1 - - + +
853B TYR 3.5 8.7 - - - +
854B ILE* 4.6 2.5 - - - -
956B ILE* 3.5 27.8 - - + -
958B ARG* 1.3 74.5 + - - +
960B VAL* 1.3 68.7 + - - +
961B PRO* 4.6 1.4 - - - +
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Residues in contact with VAL 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B HIS* 3.2 4.2 - - - -
853B TYR* 2.9 71.0 + - + +
855B ALA* 4.0 11.4 - - + -
958B ARG* 3.8 25.1 - - - +
959B VAL* 1.3 79.8 - - - +
961B PRO* 1.4 71.9 - - + +
964B THR* 3.5 22.2 - - + +
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Residues in contact with PRO 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851B SER 3.7 3.4 - - - +
852B HIS* 3.5 25.1 - - + +
853B TYR* 4.3 2.0 - - - -
959B VAL 4.6 1.1 - - - +
960B VAL* 1.4 93.4 - - + +
962B LEU* 1.3 62.2 + - - +
963B TYR* 3.6 45.3 - - + +
964B THR* 2.9 32.0 + - - +
979B LEU* 6.5 1.1 - - + -
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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