Contacts of the strand formed by residues 685 - 699 (chain A) in PDB entry 3RLN
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 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681A GLN* 2.8 23.8 + - - -
683A LYS* 3.8 11.6 + - - -
684A GLY* 1.3 76.0 - - - -
686A PHE* 1.3 74.6 + - - +
687A VAL* 4.0 13.5 - - - +
739A GLU* 3.5 7.3 + - - +
740A LEU* 3.0 27.4 + - - +
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Residues in contact with PHE 686 (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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614A LYS* 5.9 1.3 - - - -
639A ASN* 3.8 48.7 - - + +
641A PHE* 3.7 27.0 - + + -
684A GLY 6.0 0.4 - - - -
685A SER* 1.3 83.2 + - - +
687A VAL* 1.3 62.6 + - - +
688A ASN* 4.4 0.6 + - - +
737A CYS* 4.2 17.3 - - - -
738A PHE 3.3 4.5 - - - +
739A GLU* 3.7 46.0 - - + -
753A VAL* 4.4 13.5 - - + -
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Residues in contact with VAL 687 (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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673A PRO* 4.1 15.5 - - + -
678A LEU* 3.9 23.8 - - + -
681A GLN* 5.2 0.2 - - - +
685A SER* 4.0 14.6 - - - +
686A PHE* 1.3 78.7 - - - +
688A ASN* 1.3 78.8 + - - +
691A PHE* 4.5 14.1 - - + -
735A LEU* 4.4 3.4 - - + +
736A THR* 4.0 0.9 - - - -
737A CYS 3.3 5.7 + - - -
738A PHE* 2.8 38.7 + - + +
740A LEU* 4.5 4.9 - - + -
750A LEU* 3.9 24.9 - - + -
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Residues in contact with ASN 688 (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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603A THR* 4.7 1.0 + - - -
612A ARG* 3.4 47.1 - - - +
641A PHE* 5.3 5.1 - - - -
671A VAL 4.6 2.4 - - - +
673A PRO* 3.3 22.9 - - - +
686A PHE 4.4 0.9 + - - +
687A VAL* 1.3 77.9 - - - +
689A GLY* 1.3 58.6 + - - +
734A LYS* 6.3 0.7 - - - +
735A LEU 3.3 12.1 - - - +
736A THR* 3.5 16.5 + - - +
737A CYS* 3.0 24.9 + - - -
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Residues in contact with GLY 689 (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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671A VAL 5.5 0.4 - - - -
672A THR* 3.7 12.6 - - - -
688A ASN* 1.3 74.4 - - - +
690A VAL* 1.3 64.3 + - - -
691A PHE* 3.5 18.3 - - - -
733A LEU 3.4 1.9 - - - +
734A LYS* 3.4 4.4 - - - +
735A LEU* 2.7 42.0 + - - +
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Residues in contact with VAL 690 (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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670A SER 6.0 1.3 - - - +
672A THR* 3.0 28.1 + - - +
689A GLY* 1.3 74.4 - - - -
691A PHE* 1.3 63.1 + - - +
732A LYS* 4.1 29.4 - - + +
733A LEU 3.3 6.1 - - - +
734A LYS* 4.0 30.1 - - + +
761A ILE* 4.2 15.3 - - + -
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Residues in contact with PHE 691 (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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672A THR* 3.5 21.8 - - + -
673A PRO* 3.6 16.6 - - + -
675A ILE* 4.2 14.8 - - + -
678A LEU* 3.9 25.8 - - + -
687A VAL* 4.5 5.4 - - + -
689A GLY* 3.5 30.1 - - - -
690A VAL* 1.3 78.7 - - - +
692A GLU* 1.3 62.3 + - - +
693A VAL* 3.7 1.6 + - - +
707A ILE* 3.7 37.2 - - + +
708A GLN 5.5 2.0 - - - +
709A ASP* 5.2 3.6 - - + -
732A LYS* 4.1 3.6 - - - -
733A LEU* 2.7 44.2 + - + +
735A LEU* 3.9 24.5 - - + -
750A LEU* 4.5 4.9 - - + -
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Residues in contact with GLU 692 (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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690A VAL 4.4 0.4 + - - -
691A PHE* 1.3 71.7 - - - +
693A VAL* 1.3 68.6 + - - +
694A HIS 3.6 0.2 + - - -
707A ILE* 3.2 23.3 - - - +
708A GLN* 3.3 38.0 + - + +
730A GLY* 3.8 22.0 - - - +
731A ASP 3.5 13.2 - - - +
732A LYS* 3.9 23.2 - - + +
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Residues in contact with VAL 693 (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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691A PHE 4.3 1.3 - - - +
692A GLU* 1.3 75.9 - - - +
694A HIS* 1.3 58.0 + - - +
695A LYS 3.3 29.6 - - - +
696A LYS* 4.6 1.1 - - + +
705A TYR* 3.8 15.7 - - + -
706A GLU 3.7 4.3 - - - +
707A ILE* 4.4 2.7 - - + -
708A GLN* 4.6 1.1 + - - -
727A CYS* 3.6 26.0 - - - -
728A GLU 3.9 8.1 - - - +
729A GLU* 4.0 13.2 - - - +
730A GLY* 2.9 30.0 + - - -
731A ASP 2.9 16.8 + - - +
733A LEU* 3.7 24.2 - - + -
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Residues in contact with HIS 694 (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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692A GLU 3.6 3.0 + - - -
693A VAL* 1.3 74.3 - - - +
695A LYS* 1.3 86.6 + - + +
706A GLU* 2.7 29.2 + - + +
708A GLN* 3.4 45.7 - - + +
713A LYS* 5.2 9.6 + - + +
729A GLU* 3.7 19.1 - - - +
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Residues in contact with LYS 695 (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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693A VAL* 3.3 13.6 - - - +
694A HIS* 1.3 106.7 - - + +
696A LYS* 1.3 62.9 + - - +
697A ASN* 6.3 1.1 - - + -
704A TYR 4.5 0.2 - - - -
705A TYR* 3.4 1.4 - - - -
706A GLU* 2.8 46.4 + - + +
713A LYS* 5.9 1.3 - - - +
729A GLU* 3.7 12.6 - - - +
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Residues in contact with LYS 696 (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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693A VAL* 4.7 2.5 - - + -
695A LYS* 1.3 77.6 - - - +
697A ASN* 1.3 64.3 + - - +
698A VAL* 4.1 21.4 + - + +
703A THR* 4.3 8.3 - - + -
704A TYR 3.4 4.0 - - - -
705A TYR* 3.8 30.5 - - + +
725A ILE 5.1 4.8 + - - -
726A ASN* 5.4 0.8 + - - +
727A CYS 3.4 23.5 + - - +
728A GLU* 3.2 31.6 + - - +
729A GLU* 3.3 22.2 + - + +
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Residues in contact with ASN 697 (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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695A LYS* 6.3 0.9 - - + -
696A LYS* 1.3 74.9 - - - +
698A VAL* 1.3 73.5 + - - +
699A ARG* 3.5 27.9 + - - +
703A THR* 4.6 0.2 - - - -
704A TYR* 2.7 47.3 + - + +
715A GLU* 5.9 0.9 - - - +
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Residues in contact with VAL 698 (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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696A LYS* 4.1 20.4 + - + +
697A ASN* 1.3 81.5 + - - +
699A ARG* 1.3 60.5 + - - +
700A GLY 4.0 19.4 + - - +
702A PHE 3.9 2.2 - - - -
703A THR* 3.7 28.3 - - + +
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Residues in contact with ARG 699 (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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697A ASN* 3.5 26.3 + - - +
698A VAL* 1.3 76.8 - - - +
700A GLY* 1.3 63.1 + - - +
701A GLU 3.2 0.5 + - - -
702A PHE* 2.7 31.4 + - - +
704A TYR* 3.3 61.3 + - + +
715A GLU* 4.4 9.5 + - - -
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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