Contacts of the helix formed by residues 963 - 972 (chain B) in PDB entry 4E5W
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962B GLY* 1.3 73.7 - - - -
964B LEU* 1.4 53.8 + - - +
965B LYS* 3.4 15.6 + - - +
966B GLU* 3.1 29.3 + - - +
967B TYR* 2.8 35.7 + - - +
1006B ALA 3.9 3.4 - - - -
1007B ARG* 3.5 23.0 + - - +
1009B VAL 3.1 12.6 - - - -
1010B LEU* 4.1 8.4 - - - +
1011B VAL* 4.2 0.7 - - - -
1202B 0NT 4.4 5.3 + - - -
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Residues in contact with LEU 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963B SER* 1.4 71.9 - - - +
965B LYS* 1.3 58.6 + - - +
967B TYR* 4.3 2.0 - - + -
968B LEU* 2.9 55.5 + - + +
983B TYR* 4.0 16.4 - - + -
987B ILE* 4.3 10.3 - - + -
1006B ALA* 3.6 17.9 + - + +
1009B VAL* 2.8 42.5 + - + +
1011B VAL* 3.7 23.7 - - + +
1017B VAL* 3.9 12.8 - - + -
1070B THR* 5.6 1.3 - - + -
1074B LEU* 4.2 22.9 - - + -
1078B CYS* 3.6 3.0 - - - -
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Residues in contact with LYS 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963B SER* 3.1 11.4 + - - +
964B LEU* 1.3 78.3 - - - +
966B GLU* 1.3 58.6 + - + +
969B PRO* 3.2 23.6 - - - +
1006B ALA 3.7 3.2 + - - -
1007B ARG* 3.9 25.8 - - + +
1073B GLU* 4.6 13.3 + - - +
1078B CYS* 3.5 41.6 + - + +
1080B SER* 4.3 12.0 - - - +
1083B SER* 4.3 20.4 - - - -
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Residues in contact with GLU 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881B LEU 4.7 10.2 - - - +
961B SER 4.6 4.2 - - - +
962B GLY* 3.5 10.0 - - - -
963B SER* 3.1 34.8 + - - +
965B LYS* 1.3 81.0 - - + +
967B TYR* 1.3 60.9 + - - +
969B PRO* 3.7 5.1 - - - +
970B LYS* 3.4 34.6 - - - +
1202B 0NT 4.5 6.1 + - - -
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Residues in contact with TYR 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961B SER* 3.9 31.6 - - - +
963B SER 2.8 17.1 + - - +
964B LEU* 4.3 0.9 - - + -
966B GLU* 1.3 76.7 - - - +
968B LEU* 1.3 75.5 + - + +
970B LYS* 3.3 4.8 + - - +
971B ASN* 2.9 58.3 + - + +
974B LYS* 4.2 9.4 - - - +
975B ILE* 3.9 13.9 - - + +
983B TYR* 3.8 18.8 - + - -
1011B VAL* 3.7 34.8 - - + -
1014B GLU* 3.6 29.9 + - - +
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Residues in contact with LEU 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B LEU* 2.9 47.6 + - + +
967B TYR* 1.3 77.6 - - + +
969B PRO* 1.4 64.6 - - + +
971B ASN* 3.1 12.0 + - - +
972B LYS* 3.3 17.2 + - - +
975B ILE* 4.2 28.0 - - + -
980B GLN* 5.5 0.2 - - + -
983B TYR* 4.2 6.7 - - + -
1074B LEU* 3.6 45.1 - - + +
1077B TYR* 3.6 26.8 - - + +
1078B CYS* 4.0 10.8 - - - -
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Residues in contact with PRO 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B LEU 3.9 0.4 - - - +
965B LYS 3.2 25.8 - - - +
966B GLU 3.7 6.3 - - - +
967B TYR 3.7 2.7 - - - -
968B LEU* 1.4 90.2 - - + +
970B LYS* 1.3 59.8 + - + +
971B ASN 3.8 0.2 + - - -
972B LYS* 4.3 21.1 + - + +
1077B TYR 3.4 19.7 - - - +
1078B CYS* 4.0 11.2 - - + +
1079B ASP* 5.2 4.7 - - - +
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Residues in contact with LYS 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966B GLU* 3.4 27.7 - - - +
967B TYR* 3.3 9.3 + - - +
968B LEU 3.2 0.6 - - - -
969B PRO* 1.3 78.1 - - + +
971B ASN* 1.4 70.2 + - - +
972B LYS 3.8 0.7 - - - -
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Residues in contact with ASN 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967B TYR* 2.9 66.8 + - + +
968B LEU 3.1 5.9 + - - +
970B LYS* 1.4 92.2 - - - +
972B LYS* 1.4 64.1 + - - +
973B ASN* 3.2 3.1 - - - -
974B LYS* 2.8 47.4 + - + +
975B ILE* 3.1 16.7 + - + +
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Residues in contact with LYS 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968B LEU 3.3 8.6 + - - +
969B PRO* 4.3 16.2 - - - +
970B LYS 3.8 1.2 - - - -
971B ASN* 1.4 75.0 - - - +
973B ASN* 1.3 61.8 + - - +
974B LYS 3.4 0.2 + - - -
975B ILE 3.2 19.6 - - - +
1076B THR 5.5 1.3 + - - -
1077B TYR* 3.6 54.6 + - + -
1079B ASP* 5.5 10.8 + - - +
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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