Contacts of the helix formed by residues 994 - 1002 (chain B) in PDB entry 4A63
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 THR 994 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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964B HIS* 4.0 3.1 - - - -
985B VAL 4.8 0.2 - - - -
986B ASN* 3.5 30.0 + - + +
987B ALA 3.1 6.1 - - - +
988B ALA* 4.2 4.7 - - + -
992B GLY 3.7 13.5 - - - +
993B TRP* 1.3 74.2 - - - +
995B PRO* 1.4 75.8 - - - +
996B LEU* 3.6 13.9 + - - +
997B HIS* 2.9 38.8 + - + +
998B CYS* 3.2 11.6 + - - -
1017B ALA* 5.1 2.1 + - + -
1020B ALA* 4.3 16.8 - - + +
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Residues in contact with PRO 995 (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 LEU* 3.7 37.5 - - + +
964B HIS* 4.1 13.0 - - + +
967B VAL* 3.5 17.7 - - + +
984B ASN 4.7 2.5 - - - +
985B VAL 3.1 30.3 - - - +
987B ALA* 3.5 11.9 - - + +
994B THR* 1.4 84.0 - - - +
996B LEU* 1.4 50.3 + - - +
998B CYS* 3.1 12.2 + - + +
999B ALA* 2.8 32.4 + - - +
1011B LEU* 4.0 10.5 - - + -
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Residues in contact with LEU 996 (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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985B VAL 4.9 1.6 + - - +
994B THR* 3.2 10.1 + - - +
995B PRO* 1.4 73.5 - - - +
997B HIS* 1.4 60.1 + - + +
999B ALA* 3.5 1.0 + - - +
1000B ALA* 3.0 30.0 + - - +
1008B CYS* 3.7 38.3 - - + +
1011B LEU* 3.9 20.5 - - + +
1012B VAL* 4.1 9.9 - - + -
1016B ALA* 4.0 19.7 - - + -
1017B ALA 4.0 20.0 - - - +
1018B VAL* 4.1 13.0 - - + -
1029B ALA* 3.7 21.8 - - + -
1047B LEU* 4.3 11.7 - - + -
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Residues in contact with HIS 997 (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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992B GLY 4.0 13.7 - - - -
993B TRP* 3.4 28.1 - - + -
994B THR* 2.9 39.6 + - - +
996B LEU* 1.4 76.2 - - + +
998B CYS* 1.4 57.6 + - - +
1000B ALA* 3.5 2.4 + - - +
1001B SER* 3.0 22.9 + - - -
1017B ALA 5.7 0.9 - - - -
1020B ALA* 3.2 31.1 + - + -
1022B THR* 3.5 21.5 + - + +
1027B GLN 3.1 23.8 + - - -
1028B THR 3.6 1.8 - - - -
1029B ALA* 3.7 21.4 - - + +
1032B LYS* 3.8 14.7 - - + +
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Residues in contact with CYS 998 (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 HIS* 4.0 21.8 - - - -
967B VAL* 3.6 11.4 - - + -
968B CYS* 3.6 32.3 - - - -
989B ASP* 5.9 0.2 - - - -
993B TRP* 3.9 20.4 - - - -
994B THR 3.4 13.9 - - - -
995B PRO* 3.1 8.6 + - + +
997B HIS* 1.4 76.7 - - - +
999B ALA* 1.4 62.3 + - - +
1001B SER* 2.7 23.4 + - - -
1002B CYS* 3.3 14.0 - - - -
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Residues in contact with ALA 999 (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 VAL* 3.3 13.6 - - + +
995B PRO 2.8 18.4 + - - +
996B LEU 3.8 2.0 - - - +
998B CYS* 1.4 71.2 - - - +
1000B ALA* 1.3 62.5 + - - +
1002B CYS* 3.2 15.4 + - - +
1003B ASN 3.3 0.2 + - - -
1004B ASN* 3.2 21.9 + - - +
1007B VAL* 3.9 15.0 - - + -
1008B CYS* 3.8 19.5 - - - -
1011B LEU* 3.8 19.1 - - + -
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Residues in contact with ALA1000 (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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996B LEU 3.0 18.4 + - - +
997B HIS 3.6 3.6 - - - +
999B ALA* 1.3 76.1 - - - +
1001B SER* 1.4 53.7 + - - +
1003B ASN* 2.8 31.9 + - - +
1008B CYS* 3.7 8.4 - - - -
1029B ALA 3.1 28.5 - - - +
1032B LYS* 4.4 0.4 - - + -
1033B CYS* 3.4 14.9 - - - -
1043B CYS* 4.2 1.3 - - - -
1047B LEU* 3.7 17.5 - - + -
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Residues in contact with SER1001 (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 CYS* 6.0 0.3 - - - -
993B TRP* 3.8 20.8 - - - -
997B HIS 3.0 15.0 + - - -
998B CYS* 2.7 24.4 + - - -
1000B ALA* 1.4 72.2 - - - +
1002B CYS* 1.3 61.6 + - - +
1003B ASN* 4.3 0.8 - - - -
1032B LYS 3.4 20.1 + - - -
1034B GLU* 3.4 27.4 - - - +
1037B GLU* 5.5 1.6 - - - +
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Residues in contact with CYS1002 (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 VAL 4.4 9.9 - - - +
968B CYS* 4.2 23.1 - - - -
970B GLY* 6.4 0.2 - - - -
998B CYS 3.3 15.5 - - - -
999B ALA* 3.2 10.7 + - - +
1000B ALA 3.1 1.2 - - - -
1001B SER* 1.3 80.9 - - - +
1003B ASN* 1.4 68.7 + - - +
1004B ASN* 3.4 12.9 + - + +
1037B GLU* 5.8 2.2 - - - +
1038B GLU 4.7 1.9 - - - +
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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