Contacts of the strand formed by residues 996 - 1006 (chain A) in PDB entry 3HKV
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 ALA 996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861A LEU* 3.9 15.2 - - - +
865A TYR* 4.0 2.5 - - - -
902A PHE* 3.7 14.7 + - + -
920A PHE* 3.6 24.9 - - + -
947A ARG 3.3 8.5 - - - +
948A VAL* 4.2 5.2 - - + -
990A ILE* 3.6 19.7 - - + +
993A ASP 4.1 8.4 + - - +
994A THR 3.3 0.8 - - - -
995A GLN* 1.3 81.3 - - - +
997A LEU* 1.3 60.3 + - - +
998A PRO* 3.9 7.0 - - - +
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Residues in contact with LEU 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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858A HIS* 4.5 8.7 - - + +
861A LEU* 3.9 15.5 - - + -
862A GLN* 3.8 54.1 - - + +
865A TYR* 3.9 28.0 - - + -
946A ALA* 3.2 3.8 - - - -
947A ARG* 2.8 54.8 + - + +
996A ALA* 1.3 73.4 - - - +
998A PRO* 1.3 82.2 - - + +
999A THR* 3.3 11.7 + - + +
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Residues in contact with PRO 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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856A VAL* 3.8 28.2 - - + +
858A HIS* 5.9 2.4 + - + +
861A LEU* 3.9 20.9 - - + -
897A ILE* 4.3 19.7 - - + +
898A CYS 5.7 0.4 - - - +
901A GLY* 4.5 2.9 - - - -
902A PHE* 3.7 32.8 - - + -
944A PHE* 4.0 20.2 - - + -
945A VAL 3.6 6.1 - - - +
946A ALA* 4.2 0.2 - - + -
996A ALA 3.9 0.9 - - - +
997A LEU* 1.3 95.7 - - + +
999A THR* 1.3 60.2 + - - +
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Residues in contact with THR 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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855A ARG* 3.7 3.5 - - - +
856A VAL* 2.9 28.3 + - - +
884A VAL* 5.9 0.2 - - - +
945A VAL* 2.9 22.4 + - - +
946A ALA* 4.4 0.9 + - - -
947A ARG* 3.7 31.8 - - + +
997A LEU* 3.6 22.7 - - + +
998A PRO* 1.3 74.4 - - - +
1000A HIS* 1.3 91.9 + - - +
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Residues in contact with HIS1000 (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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823A LEU* 4.1 11.0 - - + -
829A GLU* 2.7 32.5 + - + -
833A VAL* 3.8 28.8 - - + +
853A VAL* 4.4 9.9 - - + -
854A GLU 3.2 15.3 - - - +
855A ARG* 4.0 8.4 - - + +
856A VAL* 3.9 6.1 - - - -
944A PHE* 3.4 7.1 - - - -
945A VAL* 2.8 44.8 + - + +
998A PRO 3.8 0.2 - - - -
999A THR* 1.3 111.4 + - - +
1001A LEU* 1.3 60.6 + - - +
1002A ILE 4.2 0.2 - - - -
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Residues in contact with LEU1001 (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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820A LEU* 4.2 20.9 - - + -
852A ARG* 6.2 0.2 - - - +
853A VAL* 3.4 3.3 - - - +
854A GLU* 2.8 56.4 + - - +
894A VAL* 3.5 31.6 - - + -
942A ALA* 4.0 14.8 - - + -
943A VAL 3.8 24.9 - - - +
944A PHE* 4.0 26.2 - - + -
1000A HIS* 1.3 75.1 - - - +
1002A ILE* 1.3 68.6 + - - +
1003A THR* 3.9 6.7 + - - +
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Residues in contact with ILE1002 (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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833A VAL* 3.9 22.4 - - + +
834A VAL* 5.6 1.3 - - + -
837A PHE* 3.6 55.0 - - + -
850A VAL* 4.3 14.4 - - + -
852A ARG 3.8 6.1 - - - +
853A VAL* 4.3 7.9 - - + -
886A TYR* 4.7 1.3 - - + -
941A LYS 3.5 2.3 - - - +
942A ALA* 3.7 1.6 - - - -
943A VAL* 2.8 44.9 + - + +
945A VAL* 3.7 26.5 - - + -
1001A LEU* 1.3 76.3 - - - +
1003A THR* 1.3 70.6 + - - +
1004A CYS* 4.4 2.7 - - + -
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Residues in contact with THR1003 (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 PO4 5.2 1.6 - - - +
850A VAL* 3.7 2.4 - - - +
851A VAL* 2.8 28.4 + - + -
852A ARG* 3.0 52.8 + - - +
854A GLU* 4.2 8.3 + - - -
940A HIS* 3.7 34.3 - - + +
941A LYS 3.3 8.3 - - - +
942A ALA* 4.8 2.6 - - - +
1001A LEU* 3.9 7.8 + - - +
1002A ILE* 1.3 72.3 - - - +
1004A CYS* 1.3 63.1 + - - +
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Residues in contact with CYS1004 (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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837A PHE* 4.2 9.4 - - + -
848A ILE* 3.7 14.8 - - + -
849A ARG 3.1 15.5 - - - +
850A VAL* 4.3 3.1 - - - -
851A VAL* 4.1 3.6 - - - +
928A VAL* 3.9 27.8 - - - -
940A HIS* 3.5 3.5 - - - -
941A LYS* 2.7 54.1 + - - +
943A VAL* 4.4 8.3 - - - -
1002A ILE* 4.4 9.4 - - + -
1003A THR* 1.3 75.3 - - - +
1005A GLU* 1.3 62.6 + - - +
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Residues in contact with GLU1005 (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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848A ILE* 3.5 9.1 - - - -
849A ARG* 2.8 74.8 + - + +
851A VAL* 3.9 15.4 - - + +
938A ASP 4.8 3.5 - - - +
939A GLY 3.6 17.0 - - - +
940A HIS* 3.9 16.3 + - + -
941A LYS* 4.4 3.6 - - - -
1004A CYS* 1.3 75.7 - - - +
1006A HIS* 1.3 70.6 + - - +
1007A VAL* 3.7 1.1 + - + -
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Residues in contact with HIS1006 (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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844A ALA* 6.3 0.9 - - + -
847A SER* 3.5 27.1 - - - -
848A ILE* 3.8 19.3 - - + +
928A VAL* 5.6 2.9 - - + -
930A ASP* 4.4 22.1 + - - -
939A GLY 4.5 2.4 + - - -
941A LYS* 4.4 9.8 - - + +
1005A GLU* 1.3 83.1 - - - +
1007A VAL* 1.3 69.2 + - - +
1008A PRO* 4.3 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