Contacts of the helix formed by residues 963 - 970 (chain A) in PDB entry 1JZ3
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 SER 963 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A TYR* 1.3 76.1 - - - +
964A GLN* 1.3 65.5 + - - +
965A GLN* 3.5 9.9 + - - +
966A GLN* 2.8 25.0 + - - +
967A LEU* 2.9 22.7 + - - +
979A GLU* 2.8 28.8 + - - -
983A TRP* 3.5 39.2 - - - -
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Residues in contact with GLN 964 (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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783A GLN* 3.3 26.9 - - - +
785A THR 5.3 0.2 - - - +
786A ARG* 3.5 0.8 - - - -
787A ALA* 3.1 27.5 + - - +
881A ARG* 3.1 21.3 + - - +
885A ASN* 5.0 3.0 - - - +
934A GLU* 3.2 21.0 + - - +
935A ASN 5.1 0.6 - - - +
958A ASN* 4.0 4.9 + - - +
962A TYR 3.8 1.4 + - - -
963A SER* 1.3 73.2 - - - +
965A GLN* 1.3 62.9 + - - +
967A LEU* 3.3 19.9 + - - +
968A MET* 3.0 37.9 + - + +
983A TRP* 5.4 1.6 - - - -
985A ASN* 3.6 28.6 - - - +
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Residues in contact with GLN 965 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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963A SER* 3.0 9.7 + - - +
964A GLN* 1.3 79.5 - - - +
966A GLN* 1.3 65.5 - - - +
968A MET* 3.3 15.8 + - + +
969A GLU* 2.8 56.2 + - + +
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Residues in contact with GLN 966 (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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962A TYR* 3.9 10.7 - - + +
963A SER* 2.8 21.9 + - - +
965A GLN* 1.3 79.7 - - - +
967A LEU* 1.3 63.5 + - - +
969A GLU* 3.0 13.2 + - + +
970A THR* 2.9 31.2 + - - +
975A LEU 4.2 0.9 - - - +
976A LEU* 3.3 17.3 - - + -
977A HIS* 2.7 69.3 + - + -
979A GLU* 2.9 30.7 + - - +
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Residues in contact with LEU 967 (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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787A ALA* 3.8 10.3 - - + -
926A TYR* 4.6 2.2 - - + -
932A PRO* 3.6 20.9 - - + +
933A SER* 3.8 20.6 - - - +
935A ASN* 3.9 22.0 - - - +
960A SER* 5.5 1.8 - - - +
962A TYR* 4.0 29.8 - - + +
963A SER 2.9 19.7 + - - +
964A GLN* 3.3 28.7 + - - +
966A GLN* 1.3 77.1 - - - +
968A MET* 1.3 54.5 + - - +
969A GLU 3.3 0.5 + - - -
970A THR 3.3 6.8 - - - +
976A LEU* 4.1 16.2 - - + -
3103A NA 2.5 28.4 - - - -
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Residues in contact with MET 968 (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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785A THR* 5.1 4.3 - - - +
786A ARG* 4.5 1.1 - - - -
787A ALA* 3.5 14.7 - - - +
788A PRO* 3.4 30.1 - - + -
816A TYR* 3.8 34.8 - - + -
964A GLN* 3.0 36.0 + - + +
965A GLN* 3.3 15.3 - - + +
967A LEU* 1.3 77.7 - - - +
969A GLU* 1.3 65.9 + - + +
970A THR 3.6 0.3 + - - -
3103A NA 4.0 7.5 - - - -
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Residues in contact with GLU 969 (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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965A GLN* 2.8 56.9 + - + +
966A GLN* 3.0 6.7 + - - +
968A MET* 1.3 88.0 - - + +
970A THR* 1.3 61.5 + - - +
971A SER 4.1 0.9 + - - -
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Residues in contact with THR 970 (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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932A PRO* 3.5 8.2 - - + +
966A GLN* 2.9 28.5 + - - +
967A LEU 3.3 2.2 - - - +
968A MET 3.4 1.0 - - - -
969A GLU* 1.3 81.2 + - - +
971A SER* 1.3 57.2 + - - +
972A HIS 3.3 24.5 - - - +
975A LEU* 3.7 24.7 + - + +
976A LEU* 3.8 20.2 - - + -
3103A NA 2.7 27.4 - - - -
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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