Contacts of the strand formed by residues 992 - 999 (chain A) in PDB entry 3I7N
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 LEU 992 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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930A VAL* 4.3 7.0 - - + +
931A LEU 5.7 0.2 - - - -
932A LEU* 4.2 19.7 - - + +
946A ALA* 4.2 6.3 - - + +
947A ARG* 3.0 19.0 + - - +
948A ASP* 3.1 58.4 - - + +
949A PHE 5.0 0.9 + - - -
965A PHE* 3.9 34.3 - - + -
977A CYS* 3.8 11.2 - - + -
978A GLN 2.8 25.1 - - - +
979A LYS* 3.9 4.3 - - - +
991A HIS* 1.3 75.4 - - - +
993A GLN* 1.3 66.6 + - - +
994A GLU* 3.9 1.0 + - - +
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Residues in contact with GLN 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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977A CYS* 3.2 3.4 - - - -
978A GLN 2.9 29.4 + - - +
980A ASP* 2.8 41.0 + - - +
988A GLU* 6.0 0.2 - - - +
991A HIS* 3.6 26.1 + - - +
992A LEU* 1.3 78.9 + - - +
994A GLU* 1.3 61.1 + - - +
995A VAL* 3.0 23.8 + - + +
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Residues in contact with GLU 994 (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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948A ASP* 2.4 34.1 - - - +
950A ASN* 3.3 23.8 - - - +
952A ASN* 3.2 24.4 + - - -
975A PHE* 3.9 9.7 - - - +
976A VAL 3.2 9.4 - - - +
977A CYS* 4.5 0.7 - - - +
992A LEU 5.1 0.2 - - - +
993A GLN* 1.3 70.1 - - - +
995A VAL* 1.3 60.2 + - - +
996A GLY 3.2 6.1 + - - +
997A LEU* 3.2 35.9 - - + +
1076A PHE* 4.6 5.7 - - - -
1081A LYS* 4.8 6.6 + - - -
1086A THR* 5.1 1.0 + - - -
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Residues in contact with VAL 995 (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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1A MET* 4.5 12.1 + - + +
2A SER* 3.1 46.8 + - - +
976A VAL* 2.9 22.6 + - + +
978A GLN* 3.2 42.0 - - + +
993A GLN* 3.0 19.0 + - + +
994A GLU* 1.3 72.2 - - - +
996A GLY* 1.3 55.1 + - - +
1086A THR* 3.7 9.6 + - - -
1087A GLY* 4.5 1.6 - - - -
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Residues in contact with GLY 996 (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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2A SER* 4.5 2.2 - - - -
975A PHE* 3.1 8.0 - - - +
976A VAL* 2.9 28.2 + - - +
994A GLU 3.2 2.8 + - - -
995A VAL* 1.3 81.3 - - - +
997A LEU* 1.3 65.7 + - - +
1086A THR* 3.2 16.5 + - - -
1087A GLY* 4.6 0.4 - - - -
1088A PHE* 3.7 15.7 - - - -
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Residues in contact with LEU 997 (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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974A LEU 3.5 6.3 - - - -
975A PHE* 4.1 2.5 - - + -
994A GLU* 3.2 40.4 - - + +
996A GLY* 1.3 84.8 - - - +
998A PHE* 1.3 66.9 + - - +
1076A PHE* 3.4 39.0 - - + -
1081A LYS* 5.2 6.3 - - - +
1083A GLU* 4.2 21.1 - - + -
1084A PRO 4.2 10.1 - - - +
1085A ALA* 3.3 4.8 - - - +
1086A THR* 3.0 37.9 + - + +
1088A PHE* 3.8 0.8 - - - +
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Residues in contact with PHE 998 (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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6A VAL* 3.7 25.8 - - + -
973A ASN* 3.5 2.9 - - - -
974A LEU* 2.8 40.9 + - + +
997A LEU* 1.3 79.0 - - - +
999A HIS* 1.3 77.7 + - - +
1000A LEU* 3.8 12.8 - - + -
1055A GLN* 5.6 0.7 - - - -
1074A ARG* 3.2 54.7 - - + -
1076A PHE* 4.0 6.6 - - - +
1085A ALA* 4.1 7.9 - - + -
1088A PHE* 3.4 40.6 - + + -
1090A ASP* 4.1 20.2 - - + -
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Residues in contact with HIS 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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60A LYS* 4.6 5.9 - - - +
83A LYS* 3.6 24.8 + - + +
971A ALA 3.5 19.1 - - - -
972A PHE* 3.5 13.8 + + + +
973A ASN* 2.7 22.9 + - - +
998A PHE* 1.3 73.5 - - - +
1000A LEU* 1.3 49.4 + - - +
1001A GLY* 3.8 14.4 - - - -
1073A TRP* 3.5 42.9 - + - +
1074A ARG* 2.6 45.6 + - - -
1075A SER 3.4 18.3 + - - +
1076A PHE 4.2 1.6 - - - +
1077A HIS* 4.5 9.0 + + + -
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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