Contacts of the strand formed by residues 874 - 883 (chain A) in PDB entry 4CEJ
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 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A ARG* 4.1 0.5 - - - -
480A SER* 2.1 29.3 + - - -
484A ILE* 4.1 11.6 - - + +
801A PHE 3.3 7.2 - - - +
804A VAL* 3.6 16.5 - - + +
870A ALA 4.4 0.2 + - - -
871A LEU 3.5 4.6 + - - +
872A THR 3.3 4.7 - - - +
873A ARG* 1.3 83.0 - - - +
875A LYS* 1.3 51.4 - - - +
877A LYS 3.2 27.4 - - - +
878A LEU* 3.7 15.3 - - + -
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Residues in contact with LYS 875 (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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479A ARG 3.4 17.5 - - - +
480A SER* 3.2 5.3 - - - -
481A ARG* 2.6 32.9 + - - +
484A ILE* 3.8 3.1 - - - +
517A TYR* 3.9 14.3 + - - +
570A TYR 5.8 2.9 + - - +
573A LYS* 5.4 8.1 - - - +
800A GLU* 3.3 50.5 + - + +
801A PHE 2.7 18.3 + - - +
802A PRO* 3.7 25.5 - - + +
874A ALA* 1.3 76.7 - - - +
876A GLU* 1.3 69.6 + - + +
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Residues in contact with GLU 876 (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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481A ARG* 2.8 38.0 + - - +
483A ASP* 5.0 0.3 - - - +
484A ILE* 3.9 9.5 - - - +
517A TYR* 3.5 22.0 + - + -
520A ASN* 4.8 0.2 - - - +
523A THR* 3.2 28.9 - - - +
567A PHE* 3.7 31.1 - - + -
568A LYS 3.8 4.7 - - - +
569A VAL* 3.9 9.4 - - - +
570A TYR 3.4 24.8 + - - +
802A PRO* 2.8 15.0 + - + +
875A LYS* 1.3 90.0 - - + +
877A LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 877 (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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484A ILE* 3.8 2.9 - - - -
522A GLU* 3.2 23.2 + - + +
523A THR* 3.5 13.9 - - - -
524A GLU 2.7 23.8 + - - +
526A GLU* 2.9 29.4 + - - +
562A LEU* 5.2 6.7 - - + -
567A PHE* 3.7 26.0 - - + -
802A PRO 3.1 4.8 + - - -
803A VAL* 3.6 27.8 - - + -
804A VAL 3.2 21.2 + - - -
874A ALA* 3.2 13.0 - - - +
876A GLU* 1.3 80.2 - - - +
878A LEU* 1.3 63.8 + - - +
879A PHE* 3.4 25.3 - - + -
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Residues in contact with LEU 878 (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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484A ILE* 3.6 21.5 - - + +
487A SER* 4.9 7.4 - - - -
488A THR* 5.1 1.1 - - - +
523A THR 5.3 0.2 + - - -
524A GLU 4.3 1.0 - - - +
525A THR* 3.5 28.8 + - + +
526A GLU* 3.0 24.8 + - - +
804A VAL* 3.5 22.0 - - + +
806A VAL* 4.9 2.7 - - + -
871A LEU* 3.7 53.2 - - + +
874A ALA* 3.7 22.0 - - + -
877A LYS* 1.3 78.3 - - - +
879A PHE* 1.3 65.1 + - - +
880A LEU* 4.5 6.3 - - + -
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Residues in contact with PHE 879 (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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526A GLU* 3.5 37.2 - - + -
528A LEU* 4.3 7.2 - - + -
558A GLU* 3.4 34.3 - - + -
562A LEU* 4.0 23.8 - - + -
803A VAL* 4.1 8.1 - - + -
804A VAL 2.9 7.4 + - - +
805A PHE* 3.4 52.8 - + + -
806A VAL* 3.0 26.4 + - - +
877A LYS* 3.4 26.9 - - - -
878A LEU* 1.3 75.9 - - - +
880A LEU* 1.3 67.6 + - - +
881A ILE* 4.1 4.5 - - + -
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Residues in contact with LEU 880 (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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491A LEU* 4.8 12.8 - - + -
525A THR* 4.5 19.1 - - + -
526A GLU 2.7 15.8 + - - +
527A LEU* 3.3 27.3 - - + +
528A LEU* 2.6 34.5 + - - +
806A VAL* 3.8 12.6 - - + -
809A LEU* 3.7 16.6 - - + -
867A LEU* 5.8 0.4 - - + -
871A LEU* 3.6 30.3 - - + -
878A LEU* 4.5 4.9 - - + -
879A PHE* 1.3 81.7 - - - +
881A ILE* 1.3 57.6 + - - +
882A GLY 4.1 0.2 + - - -
920A ILE* 4.6 19.7 - - + -
924A LEU* 5.9 1.1 - - + -
949A PHE* 5.7 3.8 - - + -
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Residues in contact with ILE 881 (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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528A LEU* 3.4 31.2 - - + +
530A ILE* 3.8 15.7 - - + -
551A GLU* 3.3 36.1 - - + +
554A ALA* 4.5 7.6 - - + -
555A ILE* 3.7 16.6 - - + +
805A PHE* 3.4 39.5 - - + -
806A VAL 3.2 13.6 + - - +
807A ALA* 3.4 9.2 - - + -
808A GLY 3.4 12.5 + - - -
809A LEU* 3.5 7.4 + - - +
879A PHE* 4.3 4.3 - - + -
880A LEU* 1.3 78.7 - - - +
882A GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 882 (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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527A LEU* 6.3 0.2 - - - +
528A LEU 3.0 10.6 + - - +
529A LEU* 3.4 7.7 - - - -
530A ILE* 3.0 23.6 + - - +
551A GLU* 3.8 6.1 - - - -
809A LEU* 3.9 6.8 - - - +
810A GLY 3.9 13.9 - - - -
880A LEU 4.1 0.4 + - - -
881A ILE* 1.3 74.6 - - - +
883A SER* 1.3 64.6 + - - -
917A LEU* 4.4 7.8 - - - +
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Residues in contact with SER 883 (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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529A LEU* 4.1 1.3 - - - -
530A ILE* 3.4 22.5 - - - +
531A ASP 6.2 0.2 - - - -
547A THR* 4.4 17.7 + - - -
551A GLU* 2.3 32.4 + - - -
594A TRP* 5.3 2.2 - - - -
810A GLY* 3.5 27.3 - - - +
882A GLY* 1.3 74.9 + - - -
884A CYS* 1.3 64.7 + - - +
890A GLN* 5.1 0.5 + - - -
917A LEU* 3.7 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