Contacts of the strand formed by residues 952 - 961 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A GLU* 5.9 0.7 - - - +
859A TYR* 3.2 4.3 - - - -
860A GLY 2.8 34.6 + - - +
929A LYS* 4.4 11.2 - - + -
930A GLY* 3.5 32.8 - - - +
950A THR* 3.9 7.6 - - - +
951A PRO* 1.3 76.8 - - - +
953A LEU* 1.3 77.7 + - + +
954A LEU* 3.3 2.4 + - + +
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Residues in contact with LEU 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A GLU* 3.9 26.0 + - + +
737A VAL* 3.9 29.4 - - + -
854A ILE* 4.9 2.0 - - + -
857A ALA* 3.8 18.4 - - + -
858A LEU 3.9 1.3 - - - +
859A TYR* 3.3 32.0 - - + +
929A LYS* 4.4 8.8 + - - +
952A VAL* 1.3 83.7 - - + +
954A LEU* 1.3 64.4 + - - +
955A GLU 3.5 26.5 - - - +
956A ILE* 4.2 14.6 - - + -
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Residues in contact with LEU 954 (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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809A ARG* 4.3 23.3 - - - +
812A LEU* 3.5 32.1 - - + -
858A LEU* 2.9 17.5 + - + +
859A TYR 3.8 2.5 - - - -
860A GLY* 3.7 22.7 - - - +
861A SER 4.2 1.3 - - - +
862A GLU* 4.0 30.2 - - + +
929A LYS* 4.1 30.3 + - + +
952A VAL 3.5 15.7 - - - +
953A LEU* 1.3 79.4 - - - +
955A GLU* 1.3 64.3 + - + +
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Residues in contact with GLU 955 (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 ARG* 5.3 0.9 + - - -
809A ARG* 3.6 34.5 + - - +
814A ARG* 4.9 2.4 + - - -
857A ALA* 3.4 6.2 - - - +
858A LEU* 2.9 51.0 + - + +
953A LEU* 3.5 3.1 - - - +
954A LEU* 1.3 79.4 - - - +
956A ILE* 1.3 63.6 + - - +
957A ASN* 3.6 23.3 + - - +
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Residues in contact with ILE 956 (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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730A TYR* 3.6 39.0 - - + +
737A VAL* 4.0 9.4 - - + -
854A ILE* 3.7 37.2 - - + -
856A GLU 4.1 2.0 - - - -
857A ALA* 4.5 0.4 - - - -
953A LEU* 4.2 14.8 - - + -
954A LEU 4.5 0.2 + - - -
955A GLU* 1.3 74.2 - - - +
957A ASN* 1.3 63.3 + - - +
958A ARG 4.1 3.6 - - - +
959A VAL* 3.6 29.2 - - + -
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Residues in contact with ASN 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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814A ARG* 3.2 32.1 + - - +
856A GLU* 2.9 27.9 + - - +
857A ALA* 3.4 18.1 - - - -
858A LEU* 3.4 1.6 + - - +
955A GLU* 3.6 33.1 + - - +
956A ILE* 1.3 73.0 - - - +
958A ARG* 1.3 67.5 + - - +
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Residues in contact with ARG 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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816A LYS* 6.0 3.8 - - - +
854A ILE* 3.8 2.4 - - - +
855A ALA* 2.9 45.5 + - + +
856A GLU* 3.1 35.5 + - + +
956A ILE* 3.6 0.4 - - - +
957A ASN* 1.3 84.5 - - - +
959A VAL* 1.3 68.9 + - - +
960A VAL* 3.8 24.2 - - - +
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Residues in contact with VAL 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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730A TYR* 3.6 26.2 - - + -
732A ASN* 4.3 11.4 - - - +
852A HIS* 3.8 26.8 - - + +
853A TYR 3.5 9.2 - - - +
854A ILE* 4.6 2.2 - - - -
855A ALA 4.4 0.2 - - - +
956A ILE* 3.6 28.3 - - + -
958A ARG* 1.3 74.1 + - - +
960A VAL* 1.3 69.5 + - - +
961A PRO* 4.6 1.6 - - - +
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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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852A HIS* 3.2 4.3 - - - -
853A TYR* 2.9 70.3 + - + +
855A ALA* 4.0 11.9 - - + -
958A ARG* 3.8 24.7 - - - +
959A VAL* 1.3 80.5 - - - +
961A PRO* 1.4 70.6 - - + +
964A THR* 3.5 22.2 - - + +
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Residues in contact with PRO 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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851A SER 3.7 4.0 - - - +
852A HIS* 3.4 26.0 - - + +
853A TYR* 4.3 2.3 - - - -
959A VAL 4.6 1.3 - - - +
960A VAL* 1.4 92.2 - - + +
962A LEU* 1.3 59.2 + - - +
963A TYR* 3.2 45.5 - - + +
964A THR* 2.9 31.8 + - - +
979A LEU* 6.4 1.6 - - + -
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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