Contacts of the helix formed by residues 985 - 1000 (chain A) in PDB entry 6Q6Q
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 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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981A MET 3.1 8.6 + - - -
982A ALA* 3.4 11.6 + - - +
983A MET 3.4 3.5 + - - -
984A SER* 1.3 82.1 - - - +
986A TYR* 1.3 67.4 + - - +
987A SER 3.6 1.3 - - - -
988A LEU* 3.6 25.0 + - - +
989A ARG* 3.3 21.5 + - - +
1184A ARG* 5.7 1.2 + - - -
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Residues in contact with TYR 986 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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946A SER* 5.3 1.8 + - - -
948A GLU* 3.0 41.0 + - + +
981A MET* 3.2 47.0 + - + +
984A SER* 4.0 9.2 - - - +
985A SER* 1.3 74.2 - - - +
987A SER* 1.3 62.7 + - - +
989A ARG* 2.8 10.5 + - - +
990A LYS* 2.7 58.6 + - + +
1007A LEU* 3.5 34.8 + - + +
1008A ALA 4.7 1.8 - - - -
1009A MET* 3.6 23.8 - - + -
1168A CYS* 4.1 8.7 - - - -
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Residues in contact with SER 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A MET* 5.3 3.1 - - - -
986A TYR* 1.3 89.4 - - - +
988A LEU* 1.3 62.3 + - - +
990A LYS* 3.9 5.5 - - - +
991A VAL* 3.3 25.1 + - - +
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Residues in contact with LEU 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985A SER* 3.6 26.4 + - - +
986A TYR 3.2 0.8 - - - -
987A SER* 1.3 78.3 - - - +
989A ARG* 1.3 60.1 + - + +
991A VAL* 3.4 21.1 - - + +
992A ALA* 3.7 10.4 + - - +
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Residues in contact with ARG 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984A SER* 2.9 33.8 + - - -
985A SER* 3.3 7.0 + - - +
986A TYR* 2.8 8.5 + - - +
988A LEU* 1.3 77.6 - - + +
990A LYS* 1.3 64.7 + - - +
991A VAL 3.4 0.4 - - - -
992A ALA* 3.6 7.5 + - + +
993A VAL* 3.2 29.0 + - + +
1007A LEU* 3.9 21.1 - - + +
1168A CYS* 4.3 5.8 - - - -
1170A GLU* 3.1 44.0 + - - +
1184A ARG* 3.2 40.1 + - - +
1186A ASP* 3.0 23.6 + - - -
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Residues in contact with LYS 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946A SER* 5.6 10.1 - - - -
948A GLU* 5.7 1.3 + - - -
986A TYR* 2.7 48.5 + - + +
987A SER* 3.4 7.8 + - - +
989A ARG* 1.3 71.5 - - - +
991A VAL* 1.3 64.6 + - - +
993A VAL* 3.3 9.7 + - + +
994A GLU* 3.2 52.0 + - - +
997A ASN* 6.0 0.6 - - - +
1007A LEU* 3.8 22.2 + - + +
1285A ASP* 3.1 34.4 + - - -
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Residues in contact with VAL 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A SER 3.3 17.5 + - - +
988A LEU* 3.4 16.6 - - + +
990A LYS* 1.3 79.5 - - - +
992A ALA* 1.3 61.5 + - + +
994A GLU* 3.4 14.8 + - + +
995A LYS* 3.0 26.5 + - + +
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Residues in contact with ALA 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A LEU 3.7 14.6 + - - +
989A ARG* 3.6 8.9 + - + +
990A LYS 3.2 0.6 - - - -
991A VAL* 1.3 83.9 - - + +
993A VAL* 1.3 56.6 + - + +
995A LYS* 3.2 13.3 + - + +
996A PHE* 3.0 24.6 + - - +
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Residues in contact with VAL 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989A ARG 3.2 19.0 + - - +
990A LYS* 3.8 11.2 - - - +
991A VAL 3.3 0.2 - - - -
992A ALA* 1.3 74.6 - - + +
994A GLU* 1.3 60.0 + - + +
996A PHE* 3.0 7.3 + - - +
997A ASN* 2.9 33.2 + - - +
1005A LYS* 3.4 43.7 - - + +
1006A GLY* 4.0 8.1 - - - +
1007A LEU* 4.6 13.2 - - + +
1170A GLU* 4.1 24.5 - - - +
1285A ASP* 4.7 4.7 - - - +
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Residues in contact with GLU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990A LYS* 3.2 45.9 + - - +
991A VAL* 3.7 13.0 - - + +
992A ALA 3.3 0.2 - - - -
993A VAL* 1.3 76.9 - - + +
995A LYS* 1.3 62.0 + - - +
997A ASN* 3.6 10.8 + - - +
998A ALA* 3.2 23.9 + - - +
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Residues in contact with LYS 995 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991A VAL* 3.0 14.3 + - + +
992A ALA* 3.3 15.0 - - + +
993A VAL 3.2 0.2 - - - -
994A GLU* 1.3 77.4 - - - +
996A PHE* 1.3 60.9 + - - +
998A ALA* 3.5 4.7 + - - +
999A GLU* 2.8 66.4 + - + +
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Residues in contact with PHE 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A SER* 4.8 2.9 - - - -
992A ALA 3.0 12.9 + - - +
993A VAL 3.0 9.1 + - - +
995A LYS* 1.3 75.2 - - - +
997A ASN* 1.3 61.7 + - - +
999A GLU* 3.1 4.7 + - - -
1000A ASN* 2.7 63.7 + - - +
1003A LYS* 3.2 36.1 - - + -
1004A LYS 4.0 0.4 - - - -
1005A LYS* 3.5 49.6 - - + -
1172A GLU* 3.9 20.9 - - - -
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Residues in contact with ASN 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990A LYS* 6.0 0.4 - - - +
993A VAL* 2.9 28.1 + - - +
994A GLU* 4.0 9.4 - - - +
995A LYS 3.4 0.2 - - - -
996A PHE* 1.3 76.7 - - - +
998A ALA* 1.3 58.6 + - - +
1000A ASN 2.9 9.5 - - - +
1004A LYS* 2.5 42.4 + - + +
1005A LYS 2.9 42.6 + - - +
1285A ASP* 5.4 2.4 + - - -
1289A ALA* 3.4 25.7 - - + +
1293A GLU* 3.5 3.3 - - - +
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Residues in contact with ALA 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A LYS* 5.9 0.7 - - - +
994A GLU 3.2 17.1 + - - +
995A LYS* 4.0 5.4 - - - +
996A PHE 3.2 0.4 - - - -
997A ASN* 1.3 76.9 - - - +
999A GLU* 1.3 61.9 + - + +
1293A GLU* 4.2 10.4 - - - +
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Residues in contact with GLU 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ASP 4.4 3.8 - - - +
548A LYS* 3.6 23.4 - - - +
995A LYS* 2.8 56.3 + - + +
996A PHE* 3.1 6.6 + - - -
998A ALA* 1.3 80.6 - - + +
1000A ASN* 1.3 69.4 + - - +
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Residues in contact with ASN1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A LYS* 4.1 4.4 - - - -
551A SER* 3.1 30.7 + - - +
996A PHE* 2.7 55.2 + - - +
997A ASN 2.9 18.5 - - - +
999A GLU* 1.3 92.7 + - - +
1001A TYR* 1.3 61.2 + - - +
1003A LYS 3.3 19.6 - - - +
1004A LYS* 3.3 12.0 + - - -
1293A GLU* 3.8 3.3 - - - +
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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