Contacts of the helix formed by residues 958 - 971 (chain A) in PDB entry 4ZTZ
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 GLY 958 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956A GLY 2.9 13.3 + - - -
957A ALA* 1.3 71.9 - - - +
959A GLN* 1.3 61.1 + - - -
960A PRO* 3.4 7.0 - - - -
961A PHE* 3.2 3.3 + - - +
962A ALA* 2.8 29.6 + - - +
3T C 4.3 21.3 - - - -
4T G 3.1 16.7 + - - -
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Residues in contact with GLN 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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957A ALA 3.4 2.8 + - - -
958A GLY* 1.3 70.4 - - - +
960A PRO* 1.4 67.4 - - + +
962A ALA* 3.9 1.2 - - - +
963A GLU* 2.9 41.0 + - - +
981A LYS* 4.9 7.8 - - + +
985A MET* 3.9 19.0 - - + +
3T C 4.8 3.2 + - - +
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Residues in contact with PRO 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A GLY* 3.6 3.4 - - - -
959A GLN* 1.4 96.3 - - + +
961A PHE* 1.3 58.7 + - + +
963A GLU* 3.2 13.4 - - + +
964A ARG* 2.8 48.8 + - - +
3T C 5.3 5.4 - - - +
4T G 6.1 1.3 - - - +
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Residues in contact with PHE 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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948A ILE* 5.8 0.7 - - + -
952A GLY* 5.1 7.4 - - - -
956A GLY 4.8 3.1 - - - -
957A ALA* 5.7 1.3 - - - -
958A GLY* 3.2 5.8 + - - +
960A PRO* 1.3 80.3 - - + +
962A ALA* 1.3 66.1 + - + +
963A GLU 3.1 0.2 + - - -
964A ARG* 3.2 24.6 - - - +
965A LEU* 2.9 63.5 + - + +
4T G 3.4 79.0 - + + +
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Residues in contact with ALA 962 (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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949A PHE* 3.7 27.8 - - + -
957A ALA* 5.0 8.3 - - + -
958A GLY 2.8 18.9 + - - +
959A GLN 4.2 0.4 - - - +
961A PHE* 1.3 78.6 - - + +
963A GLU* 1.3 57.9 + - - +
965A LEU* 4.1 4.7 - - - -
966A LEU* 2.9 33.8 + - - +
981A LYS* 4.4 5.9 - - + +
985A MET* 4.1 19.3 - - + -
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Residues in contact with GLU 963 (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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959A GLN* 2.9 33.7 + - - +
960A PRO* 3.2 13.8 - - - +
961A PHE 3.0 0.2 - - - -
962A ALA* 1.3 77.6 - - - +
964A ARG* 1.3 62.0 + - + +
967A MET* 2.9 41.8 + - + +
974A THR* 3.4 19.8 + - - +
978A ALA* 5.3 4.2 - - - +
981A LYS* 3.2 36.0 + - + +
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Residues in contact with ARG 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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623A LEU* 3.7 46.2 - - + +
760A CYS* 6.0 2.0 - - - -
761A ASN* 4.0 23.4 + - - +
762A VAL* 6.2 1.8 - - - +
960A PRO* 2.8 39.7 + - - +
961A PHE* 3.2 39.6 - - - +
963A GLU* 1.3 79.4 - - + +
965A LEU* 1.3 60.0 + - - +
967A MET* 4.1 17.0 - - + +
968A GLN* 2.9 31.3 + - - +
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Residues in contact with LEU 965 (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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623A LEU* 6.3 1.6 - - + -
948A ILE* 4.1 23.1 - - + +
949A PHE* 4.1 25.8 - - + -
952A GLY* 6.1 0.2 - - - -
961A PHE* 2.9 50.0 + - + +
962A ALA* 3.8 3.8 - - - +
964A ARG* 1.3 79.6 - - + +
966A LEU* 1.3 61.3 + - - +
968A GLN* 3.0 14.1 + - - +
969A PHE* 2.9 63.7 + - + -
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Residues in contact with LEU 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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940A GLY* 5.5 3.8 - - - +
941A ILE* 3.9 23.3 - - + -
949A PHE* 3.7 34.7 - - + -
962A ALA 2.9 20.7 + - - +
963A GLU 4.2 0.9 - - - +
965A LEU* 1.3 74.2 - - - +
967A MET* 1.3 56.4 - - - +
969A PHE* 4.5 4.7 - - + +
970A ASN* 2.9 40.8 + - + +
977A GLU* 4.7 8.7 - - + +
980A GLU* 4.3 20.9 - - + -
981A LYS* 4.3 20.2 - - + +
984A GLN* 6.1 2.2 - - + -
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Residues in contact with MET 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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759A SER* 6.4 2.2 - - - -
963A GLU* 2.9 27.9 + - + +
964A ARG* 4.1 20.4 - - + +
966A LEU* 1.3 76.5 - - - +
968A GLN* 1.3 59.3 + - - +
971A HIS* 3.1 27.5 + - - -
972A ARG 4.3 8.7 - - - +
974A THR* 3.8 36.3 - - - +
977A GLU* 3.7 28.2 - - + +
981A LYS* 5.1 0.9 - - - +
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Residues in contact with GLN 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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622A TYR* 6.1 3.3 - - + +
623A LEU* 4.3 29.8 - - + +
770A PHE* 6.3 0.8 - - - -
964A ARG 2.9 22.1 + - - +
965A LEU* 3.0 14.2 + - - +
967A MET* 1.3 78.4 - - - +
969A PHE* 1.3 80.3 + - + +
971A HIS* 3.2 30.5 + - - +
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Residues in contact with PHE 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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941A ILE* 3.3 36.4 - - + +
945A HIS* 3.5 56.3 - + + -
948A ILE* 4.4 16.6 - - + -
949A PHE* 5.9 1.8 - + + -
965A LEU* 2.9 51.2 + - + +
966A LEU* 4.1 4.3 - - + +
968A GLN* 1.3 103.0 - - + +
970A ASN* 1.3 60.3 + - - +
971A HIS* 4.6 5.1 + - - -
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Residues in contact with ASN 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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939A VAL* 3.3 9.6 + - - +
940A GLY* 2.9 35.6 + - - +
941A ILE* 4.0 12.4 - - + +
966A LEU* 2.9 24.0 + - + +
969A PHE* 1.3 77.0 - - - +
971A HIS* 1.3 71.3 + - - +
972A ARG* 3.0 41.3 + - - +
977A GLU* 4.6 10.0 + - - +
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Residues in contact with HIS 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A TYR* 5.8 11.0 - + - -
772A PRO* 3.9 33.8 - - + +
967A MET 3.1 16.3 + - - -
968A GLN* 3.2 27.0 + - - +
969A PHE 4.6 4.1 + - - -
970A ASN* 1.3 78.7 - - - +
972A ARG* 1.3 85.8 + - - +
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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