Contacts of the helix formed by residues 968 - 980 (chain A) in PDB entry 4N78
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 968 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964A ARG 4.4 0.6 + - - -
965A HIS 2.9 16.2 + - - -
966A GLU 3.0 3.0 - - - -
967A TYR* 1.3 80.4 - - - +
969A SER* 1.3 60.2 + - - -
970A PRO* 3.3 7.6 - - - -
971A GLY 3.3 0.5 + - - -
972A ILE* 3.0 31.7 + - - +
1186A VAL* 4.1 2.7 - - - -
1190A ASP* 3.6 8.5 - - - -
1192A LYS* 4.3 12.1 - - - -
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Residues in contact with SER 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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968A GLY* 1.3 70.8 - - - -
970A PRO* 1.3 75.8 - - - +
972A ILE* 3.2 2.2 + - - -
973A LEU* 2.9 22.3 + - - +
1183A LEU* 3.4 16.9 - - - +
1186A VAL* 3.7 5.7 - - - +
1187A GLN* 3.6 26.8 - - - +
1190A ASP* 2.9 26.9 + - - -
1192A LYS* 3.5 2.6 - - - +
1201A LEU* 3.2 21.0 - - - +
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Residues in contact with PRO 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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968A GLY* 3.4 4.7 - - - -
969A SER* 1.3 100.3 - - - +
971A GLY* 1.3 60.9 + - - +
973A LEU* 3.3 1.0 + - + -
974A GLU* 3.1 19.4 + - - +
1192A LYS* 3.5 29.2 - - + +
1194A GLU* 3.7 39.3 - - + +
1196A ILE* 3.5 26.9 - - + +
1201A LEU* 4.0 10.3 - - + -
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Residues in contact with GLY 971 (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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967A TYR* 4.2 16.2 + - - -
968A GLY 3.3 6.4 + - - -
970A PRO* 1.3 76.9 - - - +
972A ILE* 1.3 60.5 + - - +
974A GLU* 3.3 12.6 + - - +
975A PHE* 2.9 28.1 + - - +
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Residues in contact with ILE 972 (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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963A PRO* 3.9 25.4 - - + +
964A ARG 4.1 6.7 - - - +
967A TYR* 4.4 5.6 - - + -
968A GLY 3.0 20.8 + - - +
969A SER* 3.2 5.8 + - - +
971A GLY* 1.3 73.3 - - - +
973A LEU* 1.3 59.8 + - - +
975A PHE* 3.2 7.2 + - - +
976A PHE* 3.0 58.9 + - + -
1182A HIS* 3.9 16.2 - - + +
1183A LEU* 4.2 10.1 - - + -
1186A VAL* 3.6 38.6 - - + -
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Residues in contact with LEU 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A SER 2.9 15.9 + - - +
970A PRO 3.6 4.9 - - - +
972A ILE* 1.3 77.8 - - - +
974A GLU* 1.3 56.9 + - - +
976A PHE* 4.0 2.1 - - - +
977A HIS* 3.1 41.3 + - + +
1136A PHE* 4.0 15.5 - - + -
1183A LEU* 3.8 26.9 - - + +
1196A ILE* 3.7 22.0 - - + -
1199A VAL* 3.7 32.3 - - + +
1201A LEU* 3.8 22.7 - - + -
1204A MET* 4.4 9.4 - - + -
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Residues in contact with GLU 974 (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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970A PRO 3.1 10.3 + - - +
971A GLY* 3.6 14.3 - - - +
972A ILE 3.2 0.2 - - - -
973A LEU* 1.3 73.6 - - - +
975A PHE* 1.3 66.2 + - - +
977A HIS* 3.4 6.5 + - + +
978A HIS* 3.2 22.9 + - + +
1196A ILE* 3.5 27.8 - - + +
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Residues in contact with PHE 975 (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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960A CYS* 4.0 10.5 - - - -
961A ARG* 3.4 66.0 - - + -
963A PRO* 3.6 18.6 - - + -
971A GLY 2.9 17.6 + - - +
972A ILE* 3.5 7.0 - - - +
974A GLU* 1.3 77.6 - - - +
976A PHE* 1.3 68.6 + + - +
978A HIS* 3.3 6.7 + + + +
979A GLN* 3.0 62.2 + - + +
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Residues in contact with PHE 976 (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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960A CYS* 4.5 4.9 - - - -
961A ARG 4.3 6.5 - - - -
962A LEU* 3.9 15.5 - - + -
963A PRO* 4.3 1.6 - - + -
972A ILE* 3.0 41.5 + - + +
973A LEU* 4.0 2.9 - - - +
975A PHE* 1.3 98.9 - + - +
977A HIS* 1.3 66.7 + - - +
979A GLN* 4.5 2.0 - - - +
980A LEU* 2.9 34.5 + - + +
1136A PHE* 3.8 25.8 - + + -
1179A PHE* 3.3 61.7 - + + -
1182A HIS* 4.3 3.8 - + - -
1183A LEU* 4.3 10.3 - - + -
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Residues in contact with HIS 977 (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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973A LEU* 3.1 35.1 + - + +
974A GLU* 3.5 9.6 - - + +
975A PHE 3.3 0.2 - - - -
976A PHE* 1.3 75.7 - - - +
978A HIS* 1.3 57.7 + - - +
980A LEU 3.8 0.7 - - - -
981A LYS* 3.2 29.6 + - - +
984A VAL* 5.0 10.4 - - + +
1136A PHE* 3.8 14.4 - + - -
1140A ILE* 4.0 21.0 - - + +
1196A ILE* 3.9 9.5 + - + -
1197A LYS* 3.5 45.2 - - + +
1199A VAL* 3.2 31.7 - - + +
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Residues in contact with HIS 978 (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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974A GLU* 3.2 10.3 + - + +
975A PHE* 3.7 9.6 - + + +
976A PHE 3.2 0.6 - - - -
977A HIS* 1.3 79.5 - - - +
979A GLN* 1.3 81.7 + - + +
980A LEU 3.4 0.5 + - - -
981A LYS* 3.5 26.5 + - + +
1197A LYS* 6.2 0.9 - - - +
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Residues in contact with GLN 979 (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 PRO* 3.5 33.7 - - + +
959A ILE 3.6 22.4 + - - -
960A CYS* 4.2 16.2 - - - +
975A PHE* 3.0 54.6 + - + +
976A PHE* 3.3 4.2 + - - +
978A HIS* 1.3 93.3 - - - +
980A LEU* 1.3 62.9 + - + +
981A LYS 3.5 0.6 + - - -
982A ASP* 5.2 1.0 + - - +
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Residues in contact with LEU 980 (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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956A MET* 4.3 1.6 - - + -
957A PRO* 4.1 20.2 - - + -
960A CYS* 5.2 0.7 - - - -
976A PHE* 2.9 22.8 + - + +
977A HIS 3.8 2.5 - - - -
979A GLN* 1.3 86.5 - - + +
981A LYS* 1.3 64.3 + - - +
982A ASP 3.3 2.7 - - - -
983A ILE* 3.1 14.0 + - + +
984A VAL* 2.9 23.1 + - + +
1133A ALA* 4.0 20.9 - - + +
1136A PHE* 3.7 40.2 - - + -
1179A PHE* 3.9 35.9 - - + -
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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