Contacts of the strand formed by residues 973 - 979 (chain A) in PDB entry 3I7O
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 ASN 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967A GLY 4.2 0.2 - - - +
968A ALA* 3.5 3.1 - - - -
969A GLU* 3.1 42.2 + - - +
971A ALA* 3.2 13.1 - - - +
972A PHE* 1.3 79.6 - - - +
974A LEU* 1.3 64.0 + - - +
975A PHE* 4.7 0.5 - - - -
998A PHE 3.3 6.1 - - - +
999A HIS* 2.7 40.0 + - - +
1076A PHE* 3.7 22.0 - - + -
1077A HIS 2.7 43.9 + - - +
1078A THR* 4.2 0.2 - - - +
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Residues in contact with LEU 974 (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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6A VAL* 4.1 23.1 - - + -
966A LEU* 4.2 10.1 - - + -
967A GLY 3.4 15.0 - - - +
968A ALA* 3.6 21.3 - - + -
972A PHE 4.2 0.6 + - - -
973A ASN* 1.3 77.1 - - - +
975A PHE* 1.3 64.6 + - - +
997A LEU* 3.6 0.7 - - - -
998A PHE* 2.8 37.8 + - + +
1000A LEU* 4.0 26.9 - - + -
1004A VAL* 4.5 9.6 - - + -
1007A PHE* 4.4 5.8 - - + -
1030A PHE* 5.1 3.8 - - + -
1040A VAL* 4.6 7.0 - - + -
1076A PHE* 3.8 4.9 - - - -
1088A PHE* 4.2 20.9 - - + -
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Residues in contact with PHE 975 (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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929A SER* 3.9 4.3 - - - -
930A VAL* 4.5 8.3 - - + -
948A ASP* 4.4 1.3 - - - -
952A ASN* 3.7 26.9 - - + -
954A MET* 3.2 44.6 - - + -
965A PHE 3.6 2.0 - - - +
966A LEU* 3.4 1.9 - - - +
967A GLY* 3.0 43.0 + - - -
969A GLU* 4.3 14.6 - - + -
973A ASN 4.7 0.7 - - - -
974A LEU* 1.3 80.0 - - - +
976A VAL* 1.3 65.5 + - - +
977A CYS* 3.8 29.2 - - + -
994A GLU* 4.1 13.7 - - - +
996A GLY 3.0 14.6 - - - +
997A LEU* 4.0 11.9 - - + -
1076A PHE* 4.5 5.6 - + + -
1088A PHE* 4.5 1.3 - - - -
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Residues in contact with VAL 976 (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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2A SER* 3.6 23.6 - - - +
4A ASN* 3.7 12.3 - - - +
960A LEU* 4.6 3.6 - - + -
964A ASN* 3.9 21.8 - - + +
965A PHE 3.3 8.3 - - - +
966A LEU* 4.1 15.9 - - + -
975A PHE* 1.3 80.2 - - - +
977A CYS* 1.3 74.5 + - - +
994A GLU* 3.1 9.2 - - - +
995A VAL 2.9 22.8 + - - -
996A GLY* 2.8 11.4 + - - +
1088A PHE* 3.5 26.0 - - + -
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Residues in contact with CYS 977 (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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930A VAL* 4.4 4.7 - - + -
948A ASP* 2.9 37.2 - - - -
963A ASP 3.4 0.9 - - - +
964A ASN* 3.5 3.3 - - - +
965A PHE* 2.8 46.4 + - + +
975A PHE* 3.8 18.8 - - - -
976A VAL* 1.3 80.7 - - - +
978A GLN* 1.3 65.9 + - - +
992A LEU* 4.1 16.6 - - + -
993A GLN 3.5 4.3 - - - +
994A GLU 4.2 7.9 - - - -
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Residues in contact with GLN 978 (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* 4.0 21.9 + - - +
2A SER* 3.8 8.1 - - - +
963A ASP* 3.2 26.3 - - + +
964A ASN* 2.4 35.9 + - - +
977A CYS* 1.3 73.2 - - - +
979A LYS* 1.3 70.9 + - - +
992A LEU* 2.9 21.8 - - - +
993A GLN* 3.0 17.0 + - - +
995A VAL* 3.6 34.2 - - + +
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Residues in contact with LYS 979 (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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921A ILE* 6.3 3.1 - - - -
932A LEU* 3.5 22.9 - - + +
945A ILE* 4.0 15.3 - - + +
946A ALA* 5.7 2.5 - - + -
962A ASP 3.7 11.4 - - - +
963A ASP* 3.1 44.4 - - + +
965A PHE* 4.6 5.8 - - + -
978A GLN* 1.3 81.9 - - - +
980A ASP* 1.3 64.0 + - - +
981A SER* 3.3 7.3 + - - +
989A ARG* 5.5 12.6 - - - +
991A HIS 5.3 0.2 - - - -
992A LEU* 4.0 13.5 - - + +
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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