Contacts of the strand formed by residues 626 - 633 (chain J) in PDB entry 4XLQ
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 SER 626 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006I HIS* 5.4 0.2 + - - -
1007I ALA* 3.3 0.2 - - - -
1008I ARG* 3.0 28.5 + - - +
1028I GLY 5.1 0.3 - - - +
1029I GLY* 3.3 29.1 - - - -
1030I GLN 3.5 5.9 + - - -
623J VAL* 3.5 8.5 + - - +
624J ASP 3.6 5.5 + - - -
625J TYR* 1.3 77.1 - - - +
627J GLY* 1.3 59.7 + - - +
652J LEU* 3.3 12.6 - - - +
747J VAL 3.2 16.4 - - - -
748J HIS* 3.2 19.3 - - - -
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Residues in contact with GLY 627 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006I HIS* 3.0 14.4 - - - -
1007I ALA* 3.7 5.6 - - - +
1030I GLN* 3.5 15.6 - - - +
626J SER* 1.3 76.3 + - - +
628J ARG* 1.3 59.1 + - - -
648J MET* 3.8 7.4 - - - -
652J LEU* 4.4 1.0 - - - +
746J ALA* 3.1 8.5 - - - +
747J VAL* 2.8 30.2 + - - +
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Residues in contact with ARG 628 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004I LYS* 4.1 36.8 + - - +
1006I HIS* 2.7 36.3 + - + +
1023I GLY* 4.7 19.5 - - - +
1024I LYS* 5.1 3.8 - - - +
1030I GLN* 3.1 31.8 + - - +
622J ARG* 5.6 3.8 - - - +
627J GLY* 1.3 73.8 - - - +
629J SER* 1.3 66.4 + - - +
648J MET* 3.3 9.3 - - - +
744J GLN* 3.7 27.5 + - + +
745J MET 3.2 17.9 - - - +
746J ALA* 3.7 7.6 - - + +
747J VAL* 4.7 0.4 - - - -
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Residues in contact with SER 629 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001I VAL* 3.1 18.2 - - - +
1004I LYS* 5.4 2.5 - - - -
1005I MET* 3.6 21.3 - - - +
628J ARG* 1.3 80.4 - - - +
630J VAL* 1.3 72.0 + - - +
648J MET* 4.5 0.9 - - - -
724J GLN 3.3 10.8 + - - -
725J SER* 3.5 4.9 - - - -
726J ILE* 3.5 21.2 - - - +
744J GLN* 3.3 8.1 - - - -
745J MET* 2.9 32.1 + - - +
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Residues in contact with VAL 630 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836I GLY* 3.3 24.9 - - - +
848I VAL* 3.6 9.4 - - + -
1001I VAL* 3.5 14.2 - - + +
1004I LYS* 6.1 1.4 - - - +
629J SER* 1.3 85.5 + - - +
631J ILE* 1.3 71.5 + - - +
725J SER* 3.4 23.8 - - - -
726J ILE* 3.3 23.6 + - - +
742J GLY* 3.3 32.5 - - - +
743J ASP 3.1 16.8 - - - +
744J GLN* 4.4 2.9 - - + +
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Residues in contact with ILE 631 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848I VAL* 3.3 19.2 - - - +
630J VAL* 1.3 83.6 - - + +
632J VAL* 1.3 70.2 + - - +
726J ILE* 3.4 7.6 - - + +
728J LEU* 6.0 4.3 - - + -
733J CYS* 5.8 1.1 - - - -
738J ALA* 4.1 17.7 - - + -
739J ASP 3.1 30.3 - - - +
740J PHE* 3.4 25.1 - - + -
743J ASP* 3.8 22.9 - - + +
745J MET* 3.5 41.1 - - + -
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Residues in contact with VAL 632 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682I TYR* 5.8 1.8 - - + -
835I VAL* 4.6 3.4 - - + -
836I GLY* 4.1 2.7 - - - -
848I VAL* 5.0 1.6 - - + -
849I VAL 3.7 19.5 - - - +
850I ALA* 3.8 23.8 - - + -
851I LYS* 4.2 8.3 - - + +
631J ILE* 1.3 82.1 - - - +
633J VAL* 1.3 77.5 + - + +
725J SER* 3.3 29.8 - - - +
726J ILE 2.6 15.6 + - - +
727J GLN* 3.1 29.8 - - + -
728J LEU* 3.4 6.2 + - - +
740J PHE* 3.4 7.1 - - - -
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Residues in contact with VAL 633 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681I GLY 3.3 22.2 - - - +
682I TYR* 3.2 37.5 - - + +
684I PHE* 3.6 23.6 - - + +
687I ALA* 5.1 0.2 - - + -
850I ALA* 4.2 8.8 - - + +
632J VAL* 1.3 86.1 - - - +
634J GLY* 1.3 66.7 + - - +
635J PRO* 3.1 17.3 - - + +
727J GLN* 3.8 8.1 - - - +
728J LEU 4.2 2.0 - - - -
730J PRO* 3.8 15.3 - - + -
740J PHE* 3.2 23.1 - - + -
939J PHE* 4.9 0.2 - - + -
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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