Contacts of the helix formed by residues 963 - 971 (chain A) in PDB entry 4E4N
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 GLY* 1.3 77.1 - - - -
964A LEU* 1.3 58.2 + - - +
965A LYS* 3.2 17.0 + - - +
966A GLU* 2.9 34.0 + - - +
967A TYR* 2.9 27.4 + - - +
1006A ALA 3.8 2.7 - - - -
1007A ARG* 3.4 26.2 - - - +
1009A VAL 3.1 11.9 - - - -
1010A LEU* 3.9 8.4 - - - +
1011A VAL* 4.3 0.9 - - - -
1201A 0NL 4.5 3.5 + - - -
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Residues in contact with LEU 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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963A SER* 1.3 72.4 - - - +
965A LYS* 1.3 56.3 + - - +
967A TYR* 4.3 3.8 - - + -
968A LEU* 2.9 56.5 + - + +
983A TYR* 4.1 14.6 - - + -
987A ILE* 4.5 10.3 - - + -
1006A ALA* 3.6 21.1 + - + +
1009A VAL* 2.8 45.2 + - + +
1011A VAL* 3.7 19.9 - - + +
1017A VAL* 4.0 13.5 - - + -
1070A THR* 5.3 1.6 - - + -
1074A LEU* 4.4 18.4 - - + -
1078A CYS* 3.7 3.1 - - - -
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Residues in contact with LYS 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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963A SER* 3.1 12.2 + - - +
964A LEU* 1.3 78.2 - - - +
966A GLU* 1.3 63.7 + - - +
969A PRO* 3.1 24.3 - - - +
1006A ALA 3.9 2.0 + - - -
1007A ARG* 4.2 21.3 - - + +
1073A GLU* 4.6 11.9 + - - +
1078A CYS* 3.2 44.8 + - + +
1079A ASP 4.4 1.2 + - - -
1080A SER* 4.2 19.4 - - - +
1083A SER* 4.5 11.5 - - - -
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Residues in contact with GLU 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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881A LEU 5.2 3.7 - - - +
961A SER 4.4 6.7 - - - +
962A GLY* 4.1 4.2 - - - -
963A SER* 2.9 44.7 + - - +
965A LYS* 1.3 87.7 - - - +
967A TYR* 1.3 61.9 + - - +
968A LEU 3.6 0.2 - - - -
969A PRO* 3.6 7.6 - - - +
970A LYS* 3.5 27.4 - - + +
1201A 0NL 4.6 9.0 + - - -
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Residues in contact with TYR 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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961A SER* 3.7 37.0 - - - +
963A SER 2.9 16.7 + - - +
964A LEU* 4.3 1.1 - - + +
966A GLU* 1.3 77.6 - - - +
968A LEU* 1.3 76.6 + - + +
970A LYS* 3.1 4.1 + - - -
971A ASN* 2.8 63.7 + - + +
974A LYS* 4.0 16.3 + - - +
975A ILE* 3.9 15.2 - - + +
983A TYR* 3.8 17.7 - - - -
1011A VAL* 3.7 28.5 - - + -
1013A SER 5.7 0.2 - - - -
1014A GLU* 3.7 21.4 + - - +
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Residues in contact with LEU 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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964A LEU* 2.9 41.1 + - + +
967A TYR* 1.3 88.0 - - + +
969A PRO* 1.3 65.8 - - + +
970A LYS 3.1 1.2 + - - -
971A ASN* 3.1 10.9 + - - +
972A LYS* 3.4 17.3 + - - +
975A ILE* 4.3 20.0 - - + -
983A TYR* 4.4 2.7 - - + -
1074A LEU* 3.6 52.0 - - + +
1077A TYR* 3.7 30.3 - - + +
1078A CYS* 3.9 12.6 - - - -
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Residues in contact with PRO 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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964A LEU 3.7 1.3 - - - +
965A LYS 3.1 26.7 - - - +
966A GLU 3.6 5.8 - - - +
967A TYR 3.6 3.1 - - - -
968A LEU* 1.3 93.3 - - + +
970A LYS* 1.3 59.8 + - + +
971A ASN 3.8 0.2 + - - -
972A LYS* 4.3 19.3 + - - +
1077A TYR 3.5 17.9 - - - +
1078A CYS* 4.1 10.3 - - + +
1079A ASP* 5.5 1.3 - - - -
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Residues in contact with LYS 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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966A GLU* 3.5 20.9 - - + +
967A TYR* 3.1 8.5 + - - +
968A LEU 3.1 0.8 - - - -
969A PRO* 1.3 79.8 - - + +
971A ASN* 1.3 71.3 + - - +
972A LYS 3.8 1.3 - - - -
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Residues in contact with ASN 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* 2.8 72.0 + - + +
968A LEU* 3.1 3.7 + - - +
970A LYS* 1.3 93.1 - - - +
972A LYS* 1.3 64.1 + - - +
973A ASN 3.2 3.4 - - - -
974A LYS* 2.9 31.9 + - + +
975A ILE* 3.1 17.5 + - + +
1077A TYR* 5.4 0.2 - - - -
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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