Contacts of the helix formed by residues 986 - 1006 (chain C) in PDB entry 3H2V
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 GLU 986 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962C THR* 5.3 0.2 - - - +
966C LYS* 3.6 30.1 + - - -
982C LEU* 2.8 36.0 - - - +
983C GLN* 2.9 11.5 + - - +
985C CYS* 1.3 78.1 - - - +
987C ARG* 1.3 64.1 + - + +
988C ILE 3.2 0.4 - - - -
989C PRO* 2.8 23.4 - - - +
990C THR* 3.8 7.8 + - - -
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Residues in contact with ARG 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983C GLN* 3.6 26.7 + - - +
984C VAL* 3.4 43.4 + - - +
986C GLU* 1.3 76.0 - - + +
988C ILE* 1.3 65.3 + - - +
989C PRO* 3.2 0.2 - - - -
990C THR* 3.1 11.1 + - - -
991C ILE* 2.8 45.4 + - + +
1033C SER* 3.1 27.3 + - - +
1036C GLU* 4.2 14.5 + - - -
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Residues in contact with ILE 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958C SER* 3.4 31.6 - - - +
961C VAL* 4.4 13.0 - - + -
962C THR* 3.6 14.4 - - - +
984C VAL 3.7 15.0 - - - +
985C CYS* 3.8 9.4 - - + +
987C ARG* 1.3 76.8 - - - +
989C PRO* 1.4 60.0 - - + +
991C ILE* 3.1 6.6 + - - +
992C SER* 2.8 36.5 + - - -
1030C LEU* 4.2 10.6 - - + +
1033C SER* 4.1 8.1 - - - +
1034C VAL* 4.1 26.9 - - + +
1037C THR* 3.7 21.1 - - - +
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Residues in contact with PRO 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958C SER* 5.9 1.1 - - - -
959C ASP* 5.0 12.8 - - - +
962C THR* 4.2 19.5 - - + +
985C CYS 3.7 2.7 - - - +
986C GLU* 2.8 24.0 - - - +
987C ARG 3.2 0.4 - - - -
988C ILE* 1.4 99.9 - - + +
990C THR* 1.3 56.4 + - - +
992C SER* 2.9 21.1 + - - +
993C THR* 3.0 21.7 + - - -
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Residues in contact with THR 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986C GLU 3.8 10.4 + - - -
987C ARG* 3.1 12.6 + - - -
989C PRO* 1.3 76.6 - - - +
991C ILE* 1.3 69.3 + - + +
993C THR* 2.8 17.0 + - - -
994C GLN* 3.0 32.1 + - + +
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Residues in contact with ILE 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987C ARG* 2.8 52.7 + - + +
988C ILE* 3.7 4.5 - - - +
990C THR* 1.3 75.0 - - + +
992C SER* 1.3 63.8 + - - +
994C GLN* 3.3 13.3 + - - +
995C LEU* 3.0 9.2 + - - +
1026C ASN* 2.8 54.2 - - - +
1029C ASN* 4.3 10.1 - - + +
1030C LEU* 3.8 20.4 - - + +
1033C SER* 3.8 19.5 - - - +
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Residues in contact with SER 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951C ALA 5.4 0.2 - - - +
954C ILE* 5.2 0.6 - - - +
955C ALA* 4.2 19.0 + - - +
958C SER* 3.8 25.6 + - - -
959C ASP* 5.1 3.3 + - - -
988C ILE 2.8 14.4 + - - -
989C PRO* 2.9 23.4 + - - +
990C THR 3.1 0.2 - - - -
991C ILE* 1.3 79.7 - - - +
993C THR* 1.3 58.8 + - - +
995C LEU* 3.3 19.2 - - - +
996C LYS* 3.4 17.1 + - - +
1030C LEU* 4.5 11.9 - - - +
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Residues in contact with THR 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989C PRO 3.0 15.9 + - - -
990C THR* 2.8 8.5 + - - +
992C SER* 1.3 74.9 + - - +
994C GLN* 1.3 65.4 + - + +
995C LEU 3.0 1.6 - - - -
996C LYS* 3.0 34.4 + - - +
997C ILE* 3.0 38.6 + - + +
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Residues in contact with GLN 994 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990C THR* 3.0 34.3 + - + +
991C ILE* 3.6 13.6 - - - +
993C THR* 1.3 77.7 - - + +
995C LEU* 1.3 52.7 + - - +
997C ILE* 3.3 10.8 + - + +
998C LEU* 2.7 42.6 + - + +
1026C ASN* 2.7 34.8 + - - +
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Residues in contact with LEU 995 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930C MET* 5.1 3.1 - - + -
933C MET* 4.6 8.1 - - - -
951C ALA* 4.6 10.5 - - + +
954C ILE* 3.9 41.3 - - + -
991C ILE 3.0 12.8 + - - +
992C SER* 3.3 12.1 - - - +
993C THR 3.0 0.4 - - - -
994C GLN* 1.3 80.5 - - - +
996C LYS* 1.3 50.8 + - - +
998C LEU* 3.9 2.2 - - - +
999C SER* 2.6 39.0 + - - -
1023C LEU* 3.5 26.9 - - + +
1026C ASN* 3.5 22.4 + - + +
1027C ALA* 4.1 15.9 - - + +
1030C LEU* 4.0 10.1 - - + -
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Residues in contact with LYS 996 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948C ILE* 5.7 0.2 - - - +
951C ALA* 4.1 15.0 - - + +
952C LYS* 4.5 21.3 - - + +
955C ALA* 4.1 26.4 - - + +
959C ASP* 5.8 0.6 + - - -
992C SER* 3.4 10.2 + - - +
993C THR* 3.0 37.0 + - - +
995C LEU* 1.3 75.6 - - - +
997C ILE* 1.3 60.1 + - + +
999C SER* 2.8 18.1 + - - -
1000C THR* 2.9 22.3 + - - -
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Residues in contact with ILE 997 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993C THR* 3.0 31.6 - - + +
994C GLN* 3.5 10.3 - - + +
996C LYS* 1.3 77.2 - - + +
998C LEU* 1.3 68.6 + - + +
999C SER 3.1 1.1 - - - -
1000C THR* 3.0 12.8 + - - -
1001C VAL* 3.0 24.1 + - + +
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Residues in contact with LEU 998 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994C GLN* 2.7 21.4 + - + +
995C LEU* 3.9 1.1 - - - +
997C ILE* 1.3 75.3 - - + +
999C SER* 1.3 62.7 + - - +
1001C VAL* 3.4 15.3 - - + +
1002C LYS* 3.1 20.6 + - - +
1019C ALA 5.0 3.4 - - - +
1022C MET* 3.1 62.8 - - + +
1023C LEU* 3.8 19.6 - - + +
1026C ASN* 3.2 32.1 - - + +
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Residues in contact with SER 999 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933C MET* 4.7 2.7 - - - -
947C LEU* 4.2 23.6 - - - +
948C ILE* 4.8 4.1 - - - +
951C ALA* 3.4 17.9 - - - +
995C LEU 2.6 24.0 + - - -
996C LYS* 2.8 18.2 + - - -
998C LEU* 1.3 76.5 - - - +
1000C THR* 1.3 58.1 + - - +
1002C LYS* 3.6 1.4 - - - +
1003C ALA* 2.9 29.1 + - - +
1023C LEU* 4.0 17.0 - - - +
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Residues in contact with THR1000 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948C ILE* 4.1 20.3 - - + +
996C LYS 2.9 16.0 + - - -
997C ILE* 3.0 11.8 + - - -
999C SER* 1.3 72.6 - - - +
1001C VAL* 1.3 58.7 + - - +
1003C ALA* 3.3 6.1 + - - +
1004C THR* 2.7 45.8 + - + +
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Residues in contact with VAL1001 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997C ILE* 3.0 25.8 - - + +
998C LEU* 3.4 18.4 - - + +
1000C THR* 1.3 75.7 - - - +
1002C LYS* 1.3 69.4 - - - +
1004C THR* 3.4 9.5 + - - -
1005C MET* 3.0 35.4 + - + +
1019C ALA* 4.0 22.0 - - + -
1022C MET* 5.6 4.9 - - + -
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Residues in contact with LYS1002 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C VAL* 4.8 13.7 - - + -
947C LEU* 4.0 14.8 - - + -
998C LEU 3.1 12.5 + - - +
999C SER 3.6 5.4 - - - +
1000C THR 3.2 0.2 - - - -
1001C VAL* 1.3 84.0 - - + +
1003C ALA* 1.3 64.9 + - - +
1005C MET* 2.9 14.4 + - - +
1006C LEU* 2.9 48.7 + - + +
1016C SER* 3.3 27.7 + - - +
1019C ALA* 3.9 8.7 - - + +
1020C THR* 3.0 42.2 + - - +
1023C LEU* 3.6 19.1 - - + -
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Residues in contact with ALA1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944C LYS* 4.0 25.8 - - + +
947C LEU* 4.3 8.0 - - + +
948C ILE* 3.4 33.7 - - + -
999C SER 2.9 15.0 + - - +
1000C THR 3.4 4.5 - - - +
1001C VAL 3.3 0.2 - - - -
1002C LYS* 1.3 76.5 - - - +
1004C THR* 1.3 63.0 + - + +
1006C LEU* 3.1 29.3 + - - +
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Residues in contact with THR1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948C ILE* 6.1 0.2 - - + -
1000C THR* 2.7 31.6 + - + +
1001C VAL* 3.4 7.7 + - - -
1003C ALA* 1.3 71.7 - - + +
1005C MET* 1.3 69.0 + - - +
1006C LEU 3.4 5.2 + - - +
1008C ARG* 3.2 37.2 + - - -
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Residues in contact with MET1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001C VAL* 3.0 22.8 + - + +
1002C LYS* 2.9 18.3 + - - +
1004C THR* 1.3 78.4 + - - +
1006C LEU* 1.3 66.0 + - - +
1007C GLY 3.3 0.5 + - - -
1008C ARG* 3.1 25.4 + - - +
1011C ILE* 4.2 24.6 - - + +
1015C GLU* 4.3 32.8 - - + +
1016C SER* 4.1 18.2 - - - -
1019C ALA* 3.7 30.5 - - + -
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Residues in contact with LEU1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936C LEU 4.5 7.9 - - - +
937C VAL* 5.4 5.8 - - - +
938C ARG 5.5 0.9 - - - +
939C GLY 5.3 0.2 - - - +
940C GLY* 3.4 22.7 - - - +
941C SER* 5.5 1.6 - - - -
943C THR* 2.9 31.9 - - - +
944C LYS* 4.7 9.5 - - + +
947C LEU* 4.6 10.8 - - + -
1002C LYS* 2.9 47.5 + - + +
1003C ALA* 3.1 15.8 + - - +
1004C THR 3.4 7.8 - - - +
1005C MET* 1.3 79.5 - - - +
1007C GLY* 1.3 56.8 + - - +
1008C ARG* 3.4 3.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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