Contacts of the helix formed by residues 1004 - 1013 (chain C) in PDB entry 6GHM
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 ASN1004 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967C VAL 5.0 4.8 + - - +
970C GLY* 4.6 16.8 + - - -
972C THR* 4.9 2.9 + - - -
999C ALA* 2.9 16.6 + - - +
1002C CYS* 3.0 13.8 - - + +
1003C ASN* 1.3 72.4 - - - +
1005C VAL* 1.3 57.0 + - - +
1006C GLN* 3.3 9.7 + - - +
1007C VAL* 3.2 38.8 + - + +
1008C CYS* 2.9 30.0 + - - -
1043C CYS* 3.8 2.0 - - - -
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Residues in contact with VAL1005 (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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1003C ASN 3.2 6.1 + - - +
1004C ASN* 1.3 74.3 + - - +
1006C GLN* 1.3 71.9 + - + +
1008C CYS* 3.6 1.9 - - - +
1009C LYS* 2.8 30.8 + - + +
1039C GLY 6.1 0.2 - - - +
1042C GLN* 3.7 43.3 - - + +
1043C CYS* 3.9 20.9 - - + +
1046C PHE* 3.6 37.9 - - + -
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Residues in contact with GLN1006 (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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972C THR* 6.1 6.3 - - + +
1004C ASN* 3.2 8.6 + - - +
1005C VAL* 1.3 95.1 - - + +
1007C VAL* 1.3 58.9 + - + +
1009C LYS* 3.4 33.1 + - - +
1010C PHE* 3.0 27.7 + - - +
1042C GLN* 5.4 2.1 + - - -
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Residues in contact with VAL1007 (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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967C VAL* 4.2 19.1 - - + +
970C GLY* 5.8 2.0 - - - -
972C THR* 3.9 30.5 - - + +
975C VAL* 4.5 13.5 - - + -
999C ALA* 3.6 20.4 - - + -
1004C ASN* 3.2 33.1 + - - +
1006C GLN* 1.3 75.5 - - + +
1008C CYS* 1.3 55.6 + - - +
1010C PHE* 3.1 6.3 + - + +
1011C LEU* 2.7 48.0 + - + +
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Residues in contact with CYS1008 (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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996C LEU* 3.9 12.3 - - - +
999C ALA* 3.7 18.6 - - - -
1000C ALA* 3.7 13.2 - - - -
1004C ASN 2.9 24.1 + - - +
1005C VAL* 3.6 7.4 - - - +
1007C VAL* 1.3 78.0 - - - +
1009C LYS* 1.3 61.1 + - - +
1011C LEU* 3.3 1.3 + - - +
1012C VAL* 2.9 28.8 + - - +
1043C CYS* 3.7 20.0 - - - -
1046C PHE* 4.1 7.4 - - + -
1047C LEU* 3.9 23.3 - - + -
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Residues in contact with LYS1009 (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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1005C VAL* 2.8 21.7 + - + +
1006C GLN* 3.7 29.0 + - - +
1007C VAL 3.2 0.2 - - - -
1008C CYS* 1.3 73.0 - - - +
1010C PHE* 1.3 65.3 + - - +
1012C VAL* 3.3 2.4 + - - +
1013C GLU* 3.1 52.8 + - + +
1046C PHE* 3.6 33.8 - - + -
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Residues in contact with PHE1010 (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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972C THR* 6.4 2.0 - - + -
975C VAL* 4.1 15.3 - - + -
976C LYS* 3.7 51.1 - - + -
979C VAL* 3.7 36.6 - - + -
980C GLN* 5.4 5.4 - - + -
1006C GLN 3.0 17.4 + - - +
1007C VAL* 3.1 6.9 + - + +
1009C LYS* 1.3 78.3 - - - +
1011C LEU* 1.3 64.9 + - + +
1013C GLU* 3.4 15.1 + - + +
1014C SER* 2.7 43.0 + - - -
1120C ILE* 5.7 0.9 - - + -
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Residues in contact with LEU1011 (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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963C LEU* 4.5 2.9 - - + -
967C VAL* 4.3 1.8 - - + -
975C VAL* 4.5 12.6 - - + -
979C VAL* 4.3 16.4 - - + -
985C VAL* 3.8 22.6 - - + +
995C PRO* 3.5 42.4 - - + +
996C LEU* 3.7 11.7 - - + +
999C ALA* 4.0 3.8 - - + -
1007C VAL* 2.7 40.8 + - + +
1008C CYS 3.7 3.8 - - - +
1010C PHE* 1.3 74.7 - - + +
1012C VAL* 1.3 57.3 + - - +
1014C SER* 2.9 20.7 + - - -
1015C GLY 3.4 0.5 + - - -
1016C ALA* 3.1 28.2 + - + +
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Residues in contact with VAL1012 (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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996C LEU* 4.1 19.5 - - + -
1008C CYS 2.9 20.5 + - - +
1009C LYS* 3.8 6.1 - - - +
1011C LEU* 1.3 75.9 - - - +
1013C GLU* 1.3 62.6 + - + +
1014C SER 3.2 3.6 + - - -
1015C GLY 3.4 7.8 + - - -
1016C ALA* 3.9 10.2 + - + +
1018C VAL* 4.3 22.0 - - + -
1046C PHE* 4.6 13.9 - - + -
1047C LEU* 4.7 4.7 - - + -
1050C VAL* 4.7 11.0 - - + -
1116C LEU* 4.2 30.7 + - + +
1117C TYR* 3.8 16.1 + - + +
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Residues in contact with GLU1013 (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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1009C LYS* 3.1 53.8 + - + +
1010C PHE* 3.7 16.3 - - + +
1012C VAL* 1.3 77.6 - - + +
1014C SER* 1.3 59.3 + - - +
1015C GLY 3.6 0.7 - - - -
1117C TYR* 3.7 39.3 + - + +
1118C PRO 4.7 1.0 - - - +
1120C ILE* 5.0 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