Contacts of the strand formed by residues 707 - 715 (chain A) in PDB entry 4J2E
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 ARG 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702A TRP* 3.6 0.7 - - - -
703A THR* 3.1 45.0 + - - +
704A GLY* 3.2 13.3 + - - +
705A LYS 3.2 4.6 - - - +
706A LYS* 1.3 84.4 - - - +
708A TYR* 1.3 65.5 + - - +
728A MET 3.3 5.2 - - - -
729A GLY 3.7 18.6 + - - +
730A LEU* 3.6 23.6 - - + +
731A GLU* 3.1 37.6 + - - -
734A LYS* 5.6 1.8 - - - +
879A PRO* 5.3 3.2 + - - +
882A GLY* 5.9 2.8 - - - -
883A PHE* 3.8 10.7 - - - -
9T G 3.2 33.1 - - - +
10T C 3.5 25.1 + - - -
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Residues in contact with TYR 708 (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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619A TYR* 4.0 15.5 - + - -
626A TYR* 2.7 35.7 + + - -
701A PHE* 3.3 16.2 - - - +
702A TRP* 3.3 38.8 - + + +
703A THR 4.9 0.4 - - - +
706A LYS 4.8 0.4 - - - -
707A ARG* 1.3 86.2 - - - +
709A ALA* 1.3 64.7 + - - +
710A LEU* 4.3 13.0 - - + -
726A LYS* 3.4 10.0 + - + -
727A ILE* 3.6 3.1 - - - +
728A MET* 2.9 64.4 + - + +
730A LEU* 3.9 8.7 - - - +
114P A 4.5 1.3 - - - -
115P G 2.5 30.1 + - - -
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Residues in contact with ALA 709 (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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700A GLY* 3.2 4.2 - - - -
701A PHE* 3.0 49.4 + - + +
708A TYR* 1.3 76.2 - - - +
710A LEU* 1.3 65.2 + - - +
726A LYS 3.3 6.5 - - - -
727A ILE* 4.0 12.3 - - + -
730A LEU* 4.2 3.8 - - + +
749A ILE* 3.8 28.7 - - + -
753A LEU* 3.9 3.8 - - + -
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Residues in contact with LEU 710 (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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407A VAL* 4.0 25.1 - - + -
626A TYR* 3.8 33.2 - - + -
687A ALA* 5.2 5.6 - - + -
689A ALA* 3.9 16.2 - - + -
699A GLY 3.8 3.6 - - - +
700A GLY* 4.1 9.9 - - - -
702A TRP* 3.7 27.6 - - + -
708A TYR* 4.3 10.3 - - + -
709A ALA* 1.3 80.5 - - - +
711A ASN* 1.3 59.4 + - - +
712A VAL* 3.5 10.3 + - + +
725A LEU* 3.5 4.2 - - - -
726A LYS* 2.8 47.9 + - + +
727A ILE* 5.4 0.2 - - - +
753A LEU* 3.6 5.5 - - - +
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Residues in contact with ASN 711 (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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689A ALA* 3.2 3.3 - - - +
690A GLY 2.9 47.8 + - - +
691A PRO* 4.3 0.2 - - - +
692A PRO* 3.9 11.9 - - - +
699A GLY 2.9 21.0 + - - +
710A LEU* 1.3 70.6 - - - +
712A VAL* 1.3 60.0 + - - +
713A TRP* 3.5 25.5 - - - +
723A PRO* 3.5 10.0 - - - +
724A LYS 4.0 2.4 - - - +
725A LEU* 3.8 6.1 - - - +
753A LEU* 3.6 15.9 - - + +
754A GLN* 2.8 35.4 + - - +
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Residues in contact with VAL 712 (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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687A ALA* 3.9 22.2 - - + -
688A ILE 3.5 7.6 - - - +
689A ALA* 4.3 2.5 - - + -
710A LEU* 3.8 14.1 - - + +
711A ASN* 1.3 75.0 - - - +
713A TRP* 1.3 63.5 + - - +
714A ASP 3.4 28.3 - - - +
715A MET* 4.1 9.0 - - + -
720A TYR* 3.6 15.8 - - + -
723A PRO* 3.5 4.0 - - - +
724A LYS* 2.8 40.8 + - + +
726A LYS* 3.7 29.6 - - + -
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Residues in contact with TRP 713 (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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644A THR* 3.5 32.1 - - + -
645A ASN* 6.4 0.4 - - - -
647A TRP* 3.7 20.2 - + - -
648A VAL* 3.7 23.3 - - + -
688A ILE 2.9 11.8 + - - +
690A GLY 2.8 23.6 + - - -
692A PRO* 3.7 27.1 - - + -
711A ASN* 3.5 29.6 - - - +
712A VAL* 1.3 73.0 - - - +
714A ASP* 1.3 61.7 + - - +
719A ARG* 3.6 8.3 - - - -
720A TYR* 3.2 36.3 + - - +
721A ALA 6.0 0.7 - - - -
722A GLU 5.3 0.7 - - - -
723A PRO* 3.7 39.5 - - + -
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Residues in contact with ASP 714 (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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648A VAL* 4.2 10.5 - - + -
685A ARG* 2.8 40.4 + - - +
687A ALA* 3.3 2.3 - - - -
688A ILE* 3.0 31.3 + - + -
712A VAL* 3.4 4.5 - - - +
713A TRP* 1.3 81.3 - - - +
715A MET* 1.3 61.2 + - - +
717A GLY* 3.2 17.7 + - - -
718A THR 3.2 10.1 - - - -
719A ARG* 2.6 43.6 + - - +
720A TYR* 4.7 0.2 - - - -
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Residues in contact with MET 715 (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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490A LEU* 5.4 0.3 - - - +
493A GLN* 4.4 4.8 - - - +
686A GLU* 3.4 33.2 - - - +
687A ALA* 3.9 19.1 - - + -
712A VAL* 4.1 10.5 - - + -
714A ASP* 1.3 73.8 + - - +
716A GLU* 1.3 77.2 + - + +
717A GLY 3.1 1.1 - - - -
718A THR* 2.8 28.3 + - - -
720A TYR* 3.2 31.8 - - + +
726A LYS* 3.9 31.0 - - + -
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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