Contacts of the strand formed by residues 938 - 945 (chain A) in PDB entry 4ZZ0
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 VAL 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918A LEU* 4.3 10.8 - - + +
922A PHE* 5.6 0.7 - - - -
936A VAL* 3.5 19.8 - - - +
937A THR* 1.3 93.2 + - - +
939A THR* 1.3 73.9 + - - +
960A ALA* 3.9 19.1 - - + -
961A VAL 3.7 6.1 - - - +
962A PRO* 5.1 4.5 - - + -
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Residues in contact with THR 939 (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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916A PRO 4.3 3.3 + - - -
917A SER* 4.1 12.5 - - - -
918A LEU* 3.4 16.6 + - - +
922A PHE* 4.8 4.0 - - - -
928A HIS* 5.4 1.7 + - - +
931A ALA* 4.2 12.0 - - - +
936A VAL* 4.4 7.6 - - - -
938A VAL* 1.3 76.2 - - - +
940A GLY* 1.3 69.3 + - - +
960A ALA* 3.3 7.4 - - - -
961A VAL 2.8 34.0 + - - +
963A VAL* 3.7 20.4 - - + +
972A LEU* 3.8 24.0 - - + -
976A VAL* 4.0 11.7 - - + -
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Residues in contact with GLY 940 (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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916A PRO 3.1 7.4 - - - +
917A SER* 3.1 23.7 + - - -
918A LEU* 3.8 5.8 - - - +
939A THR* 1.3 86.0 + - - +
941A CYS* 1.3 62.0 + - - +
959A GLU 3.1 13.5 - - - -
961A VAL* 3.8 12.6 - - - -
976A VAL* 3.6 9.0 - - - +
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Residues in contact with CYS 941 (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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914A ILE* 4.4 1.8 - - + -
915A HIS 3.3 10.1 - - - +
916A PRO* 4.1 0.7 - - + -
917A SER 3.3 4.9 - - - -
918A LEU* 3.8 1.4 - - - +
940A GLY* 1.3 76.7 - - - +
942A THR* 1.3 65.5 + - - +
958A GLN* 3.2 6.9 - - - +
959A GLU* 3.0 32.9 + - - -
976A VAL* 3.9 6.1 - - + -
979A ALA* 3.7 17.5 - - - -
980A GLU* 3.5 45.1 - - + -
983A ILE* 3.5 20.8 - - + +
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Residues in contact with THR 942 (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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913A ASN 3.6 1.0 - - - +
914A ILE* 3.4 3.7 - - - +
915A HIS* 2.9 32.8 + - - +
917A SER 2.7 21.6 + - - -
919A LEU* 3.1 30.3 + - + -
941A CYS* 1.3 73.6 - - - +
943A VAL* 1.3 76.3 + - - +
944A HIS* 4.1 3.0 + - + -
955A ILE* 4.0 14.4 - - + -
957A LEU 3.5 4.3 - - - -
958A GLN* 3.0 34.3 + - + +
983A ILE* 4.0 0.9 - - - -
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Residues in contact with VAL 943 (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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912A LEU* 4.1 15.3 - - + -
913A ASN 3.2 9.9 - - - +
914A ILE* 3.5 25.1 - - + -
942A THR* 1.3 75.2 - - - +
944A HIS* 1.3 62.5 + - - +
955A ILE 3.8 0.2 - - - -
956A ILE* 2.8 27.3 + - + +
957A LEU 2.9 16.2 + - - +
983A ILE* 3.7 20.6 - - + +
984A PHE* 3.8 30.3 - - + -
987A ALA* 3.6 24.5 - - + -
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Residues in contact with HIS 944 (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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912A LEU* 3.4 2.1 - - - -
913A ASN* 2.9 75.0 + - + -
915A HIS* 4.5 1.1 - - + +
919A LEU* 3.7 21.1 - - + +
942A THR* 4.3 9.4 - - + -
943A VAL* 1.3 76.7 - - - +
945A PHE* 1.3 84.4 + - - +
946A VAL* 4.5 0.9 - - - -
951A ASP* 3.8 19.5 + - - -
953A GLY 3.7 17.4 + - - +
954A GLN 3.2 14.8 - - - +
955A ILE* 4.0 4.9 - - + -
956A ILE* 4.1 7.4 - - - +
1102A 3YE 3.6 24.2 - - - -
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Residues in contact with PHE 945 (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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909A GLY* 3.3 35.4 - - - +
911A MET 3.4 13.7 - - - -
912A LEU* 4.2 7.6 - - + -
944A HIS* 1.3 87.1 + - - +
946A VAL* 1.3 61.9 + - - +
953A GLY* 3.1 18.2 - - - -
954A GLN* 2.8 24.1 + - + +
956A ILE* 3.7 22.6 - - + +
991A VAL* 3.8 29.2 - - + -
996A VAL* 4.2 6.5 - - + -
997A GLN* 4.2 10.3 - - - -
998A LEU* 3.8 51.4 - - + -
1004A ILE* 4.8 4.0 - - + -
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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