Contacts of the helix formed by residues 994 - 1007 (chain B) in PDB entry 3E0D
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 ASP 994 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992B PRO 3.7 2.2 + - - -
993B LEU* 1.3 76.0 - - - +
995B GLU* 1.3 61.1 + - - +
997B THR* 3.0 30.5 + - - +
998B MET* 2.9 28.0 + - - +
1017B ARG* 2.4 55.5 + - + +
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Residues in contact with GLU 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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994B ASP* 1.3 73.3 - - - +
996B ILE* 1.3 58.5 + - - +
998B MET* 3.7 10.3 - - + +
999B LEU* 2.8 45.7 + - + +
1012B GLY* 6.0 0.3 - - - -
1013B HIS 4.7 6.4 + - - +
1014B PRO 4.2 2.5 - - - -
1016B LEU* 4.2 33.6 - - - +
1017B ARG* 4.5 10.7 - - + +
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Residues in contact with ILE 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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994B ASP 3.4 0.4 - - - -
995B GLU* 1.3 75.3 - - - +
997B THR* 1.3 58.9 + - - +
999B LEU* 3.4 2.1 + - - +
1000B ARG* 2.8 41.8 + - + +
1014B PRO* 3.2 21.5 - - + +
1017B ARG* 1.9 81.4 - - + +
1018B TYR* 2.8 44.9 - - + +
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Residues in contact with THR 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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993B LEU* 3.8 23.3 - - + -
994B ASP* 3.0 42.6 + - - +
996B ILE* 1.3 79.1 - - - +
998B MET* 1.3 63.1 - - - +
1000B ARG* 3.4 13.3 - - - +
1001B TYR* 3.1 47.2 + - + -
1017B ARG* 5.4 1.1 - - - -
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Residues in contact with MET 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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950B ARG* 3.6 28.1 + - - +
993B LEU* 4.2 24.5 - - + +
994B ASP 2.9 20.0 + - - +
995B GLU* 3.7 9.9 - - + +
997B THR* 1.3 76.9 - - - +
999B LEU* 1.3 91.6 + - + +
1001B TYR* 3.3 4.9 + - - +
1002B GLU* 3.1 48.8 + - - +
1011B SER* 4.5 5.6 - - - +
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Residues in contact with LEU 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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995B GLU* 2.8 24.7 + - + +
996B ILE 3.8 0.7 - - - +
998B MET* 1.3 84.5 - - + +
1000B ARG* 1.3 62.9 + - - +
1002B GLU* 3.4 10.6 + - - +
1003B LYS 3.3 10.7 + - - -
1009B TYR* 3.2 26.3 - - + -
1010B VAL 4.3 0.9 - - - +
1011B SER 3.3 12.3 - - - +
1012B GLY 2.5 30.3 - - - +
1013B HIS* 1.8 24.5 - - - +
1014B PRO* 1.5 91.8 - - + -
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Residues in contact with ARG1000 (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 ILE* 2.8 29.6 + - + +
997B THR* 3.4 15.9 - - - +
998B MET 3.2 0.2 - - - -
999B LEU* 1.3 77.9 - - - +
1001B TYR* 1.3 69.0 + - + +
1003B LYS* 3.5 4.3 + - - +
1004B GLU* 3.2 22.3 + - + +
1009B TYR* 4.4 6.7 - - - -
1014B PRO* 4.5 0.8 - - - +
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Residues in contact with TYR1001 (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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940B LYS* 3.7 55.0 - - + +
950B ARG* 5.7 1.1 - - - +
954B LEU* 4.4 13.1 - - + +
993B LEU* 4.1 36.3 - - + -
997B THR* 3.1 32.0 + - - -
998B MET* 3.7 6.5 - - - +
999B LEU 3.3 0.2 - - - -
1000B ARG* 1.3 80.8 - - + +
1002B GLU* 1.3 65.5 + - - +
1004B GLU* 3.2 15.3 + - - +
1005B ALA* 3.0 23.9 + - - +
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Residues in contact with GLU1002 (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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870B PRO* 4.4 4.3 - - - +
940B LYS 3.7 10.5 + - - +
941B ALA* 4.0 14.8 - - - +
950B ARG* 3.6 26.4 + - - +
998B MET* 3.1 35.2 + - - +
999B LEU* 3.5 13.1 - - - +
1001B TYR* 1.3 75.2 - - - +
1003B LYS* 1.3 51.9 + - - +
1005B ALA* 3.0 3.2 + - - +
1006B LEU* 2.7 41.1 + - + +
1008B ILE 3.8 8.1 - - - +
1009B TYR* 4.8 1.3 - - - -
1010B VAL* 2.6 45.8 - - - +
1011B SER* 4.8 0.5 - - - -
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Residues in contact with LYS1003 (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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999B LEU 3.3 2.8 + - - -
1000B ARG* 3.7 6.5 - - - +
1001B TYR 3.3 0.2 - - - -
1002B GLU* 1.3 77.7 - - - +
1004B GLU* 1.3 58.9 + - - +
1007B GLY* 2.6 54.5 + - - +
1008B ILE* 3.4 14.7 + - - -
1009B TYR* 3.6 29.8 - - + +
1095B GLU* 3.6 14.6 + - - -
1096B ASP* 1.2 118.4 + - - +
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Residues in contact with GLU1004 (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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895B LYS* 3.5 19.4 - - - +
896B ASN* 5.1 10.5 + - - +
937B SER* 5.2 3.7 + - - -
940B LYS* 2.9 35.9 + - - +
1000B ARG* 3.2 11.7 + - + +
1001B TYR* 3.2 17.7 + - - +
1003B LYS* 1.3 78.6 - - - +
1005B ALA* 1.3 57.4 + - - +
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Residues in contact with ALA1005 (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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894B VAL* 3.4 7.4 - - - -
895B LYS* 2.8 34.5 + - - +
937B SER* 3.6 33.0 - - - +
940B LYS* 3.8 7.4 - - + -
941B ALA* 3.7 16.4 - - + +
1001B TYR 3.0 16.1 + - - +
1002B GLU 3.0 3.1 + - - +
1004B GLU* 1.3 77.5 - - - +
1006B LEU* 1.3 59.5 + - - +
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Residues in contact with LEU1006 (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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851B SER* 5.3 2.9 + - - +
854B VAL* 5.5 4.9 - - - +
870B PRO* 5.0 0.2 - - + -
871B PRO* 3.8 24.2 - - + -
889B PHE* 4.4 14.2 - - + -
893B ALA* 3.4 41.4 - - + +
894B VAL* 4.0 12.3 - - + +
895B LYS* 4.4 7.0 - - - -
941B ALA* 3.9 20.0 - - + +
1002B GLU* 2.7 22.6 + - - +
1005B ALA* 1.3 79.1 - - - +
1007B GLY* 1.3 54.6 + - - +
1008B ILE* 3.0 27.5 + - + +
1010B VAL* 4.1 23.1 - - + -
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Residues in contact with GLY1007 (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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851B SER* 5.3 7.4 - - - -
895B LYS* 4.0 19.5 - - - +
1003B LYS* 2.6 44.6 + - - +
1005B ALA 3.8 0.4 - - - -
1006B LEU* 1.3 70.4 - - - +
1008B ILE* 1.3 61.5 + - - +
1095B GLU* 5.2 1.7 - - - +
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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