Contacts of the strand formed by residues 971 - 977 (chain A) in PDB entry 4RIB
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 PHE 971 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A PHE* 4.7 2.9 - - - -
931A LEU* 5.4 1.8 - - + -
934A CYS* 3.0 43.5 - - + -
935A LEU* 3.5 35.4 - - + -
939A VAL* 4.7 6.5 - - + -
962A VAL* 5.1 6.1 - - + -
963A VAL 3.3 10.1 - - - +
964A TRP* 3.7 11.4 - - + +
969A ARG 4.6 1.6 - - - -
970A HIS* 1.3 75.8 - - - +
972A LYS* 1.3 70.5 + - - +
973A LEU* 4.3 13.0 - - + -
998A GLY 5.0 1.6 - - - -
999A ALA* 3.6 34.8 - - + -
1000A GLU* 3.1 31.0 - - - +
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Residues in contact with LYS 972 (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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822A TYR* 3.9 19.1 - - + -
827A PHE* 3.6 30.4 - - + -
961A LEU 4.0 0.2 - - - +
962A VAL* 3.5 3.1 - - - -
963A VAL* 2.6 54.9 + - + +
971A PHE* 1.3 75.5 - - - +
973A LEU* 1.3 62.9 + - - +
974A VAL* 4.1 5.1 + - + -
1000A GLU* 3.4 38.5 + - + +
1002A GLU* 3.2 32.0 + - + +
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Residues in contact with LEU 973 (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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838A PHE* 3.6 19.3 - - + -
935A LEU* 5.1 4.5 - - + -
939A VAL* 6.2 0.9 - - + -
959A PRO* 4.1 10.8 - - + -
961A LEU 3.5 2.9 - - - +
962A VAL* 3.5 41.1 - - + -
971A PHE* 4.3 14.1 - - + -
972A LYS* 1.3 70.1 - - - +
974A VAL* 1.3 62.7 + - - +
991A LEU* 5.3 1.4 - - + +
994A LEU* 3.8 36.1 - - + -
999A ALA* 4.4 11.9 - - + -
1000A GLU 2.8 12.3 + - - +
1001A VAL* 3.4 14.8 - - + +
1002A GLU* 2.8 27.9 + - - +
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Residues in contact with VAL 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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822A TYR* 3.7 33.4 - - + +
959A PRO* 3.6 5.0 - - - +
960A ASP 3.3 1.4 + - - -
961A LEU* 2.8 53.3 + - + +
963A VAL* 4.4 7.0 - - + -
972A LYS* 4.3 13.2 - - + +
973A LEU* 1.3 79.6 - - - +
975A GLU* 1.3 61.7 + - - +
976A VAL* 3.7 17.8 + - + -
1002A GLU* 3.2 10.5 - - + +
1004A CYS* 3.8 28.9 - - + -
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Residues in contact with GLU 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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958A LEU 3.7 3.3 - - - +
959A PRO* 3.4 16.2 - - + +
960A ASP* 2.2 43.5 + - - +
973A LEU 4.3 0.2 + - - -
974A VAL* 1.3 73.5 - - - +
976A VAL* 1.3 61.0 + - - +
977A LYS* 3.3 19.8 + - + -
983A LEU* 4.1 12.1 - - + -
987A GLN* 3.0 33.5 + - + +
991A LEU* 5.0 12.9 - - + +
1002A GLU 3.0 9.5 + - - +
1003A VAL* 3.5 7.1 - - - +
1004A CYS 2.9 25.1 + - - -
1101A CA 2.3 15.4 - - - -
4U C 3.7 0.7 + - - -
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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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814A VAL* 3.6 44.0 - - + +
815A GLU* 4.2 16.8 - - + +
818A ALA* 3.6 16.4 - - + -
960A ASP* 3.6 8.0 + - + +
961A LEU* 3.5 31.4 - - + -
974A VAL* 3.7 8.5 + - + -
975A GLU* 1.3 75.7 + - - +
977A LYS* 1.3 61.8 + - - +
978A GLY 4.2 1.0 + - - -
1004A CYS 3.5 8.7 - - - +
1006A VAL* 4.9 2.0 - - + -
1101A CA 2.3 31.7 - - - -
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Residues in contact with LYS 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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975A GLU* 3.3 21.2 + - + -
976A VAL* 1.3 82.6 - - - +
978A GLY* 1.3 67.0 + - - +
981A ASP* 2.9 31.8 + - - +
982A ARG* 3.0 27.4 + - - +
983A LEU* 3.6 11.0 - - + +
987A GLN* 3.0 25.5 + - - +
1003A VAL* 4.3 18.4 - - + -
1004A CYS 3.0 8.8 + - - +
1005A HIS* 3.2 21.6 - - + +
1006A VAL* 2.9 26.7 + - - +
1101A CA 4.1 0.2 - - - -
4U C 3.3 11.1 + - - -
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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