Contacts of the strand formed by residues 697 - 705 (chain A) in PDB entry 3LJ1
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 697 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A SER* 3.1 2.8 - - - -
694A PHE* 2.7 49.2 + - + +
695A GLN* 3.4 4.1 + - + +
696A GLY* 1.3 73.8 - - - +
698A PRO* 1.3 69.1 - - + +
699A VAL* 3.4 10.3 + - + +
730A ARG* 3.4 25.7 - - - +
732A TYR* 3.3 39.2 + - + -
810A ARG* 3.4 25.1 - - - +
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Residues in contact with PRO 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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691A GLN* 6.1 0.4 - - + -
692A GLY 3.5 9.9 - - - +
693A SER* 4.2 2.7 - - - -
696A GLY 3.2 7.6 - - - +
697A ARG* 1.3 84.3 - - + +
699A VAL* 1.3 64.7 + - - +
732A TYR* 5.1 2.6 + - - -
747A LEU* 3.8 26.8 + - + +
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Residues in contact with VAL 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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692A GLY 2.8 33.2 + - - +
693A SER* 3.5 31.4 - - - +
694A PHE* 3.7 13.2 - - + +
697A ARG* 3.9 9.4 - - + +
698A PRO* 1.3 79.7 - - - +
700A ALA* 1.3 58.6 + - - +
701A VAL* 4.1 12.8 - - + -
732A TYR* 3.4 28.0 - - + -
744A ALA* 4.2 7.6 - - + -
745A LEU 3.1 24.0 - - - +
747A LEU* 3.8 9.2 - - - +
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Residues in contact with ALA 700 (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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1A DKI 3.4 33.7 - - + +
680A LEU* 3.5 25.6 - - + -
689A VAL* 4.1 7.4 - - + -
690A PHE 3.5 5.2 - - - -
699A VAL* 1.3 71.4 - - - +
701A VAL* 1.3 61.3 + - - +
702A LYS 3.8 0.2 + - - -
743A ILE 3.5 1.9 - - - +
745A LEU* 2.8 36.1 + - + +
746A GLU 4.2 0.7 - - - +
747A LEU* 3.6 6.3 - - - +
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Residues in contact with VAL 701 (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 LEU* 4.2 16.6 - - + -
674A VAL 4.8 1.3 - - - +
675A VAL* 3.8 27.8 - - + -
689A VAL* 3.3 2.6 - - - -
690A PHE* 2.8 42.8 + - + +
692A GLY* 4.3 11.2 - - - -
699A VAL* 3.6 22.9 + - + +
700A ALA* 1.3 74.1 - - - +
702A LYS* 1.3 61.6 + - - +
703A ARG* 3.8 0.9 + - + -
742A TYR* 3.7 41.5 - - + -
743A ILE 3.4 6.5 - - - +
744A ALA* 4.7 0.9 - - - -
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Residues in contact with LYS 702 (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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1A DKI 5.5 6.0 - - - -
687A THR* 3.8 30.1 - - + -
688A VAL 3.9 2.5 - - - -
689A VAL* 4.0 16.6 - - + +
700A ALA 3.8 0.2 + - - -
701A VAL* 1.3 71.8 - - - +
703A ARG* 1.3 59.7 + - - +
704A MET* 3.8 16.5 + - + +
715A GLU* 2.8 40.7 + - - +
741A LEU 3.7 2.3 - - - +
742A TYR* 3.6 1.6 - - - -
743A ILE* 2.7 52.3 + - + +
745A LEU* 4.6 19.3 - - + -
828A ASP* 3.7 25.9 + - - +
830A GLY* 4.7 1.6 - - - +
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Residues in contact with ARG 703 (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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666A PHE* 4.4 8.1 - - - +
667A GLU* 2.8 33.1 + - - -
686A GLY 4.0 5.3 + - - +
687A THR* 3.4 8.4 - - - +
688A VAL* 2.9 50.5 + - - +
690A PHE* 3.9 27.6 - - + -
701A VAL 3.8 1.2 + - - +
702A LYS* 1.3 69.9 - - - +
704A MET* 1.3 62.1 + - - +
740A PHE* 3.6 40.8 - - + -
741A LEU 4.0 2.2 - - - -
742A TYR* 3.4 40.2 - - + -
685B SER* 4.5 7.9 - - - +
686B GLY* 4.2 19.2 - - - +
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Residues in contact with MET 704 (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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684A SER 5.3 3.1 - - - +
685A SER* 5.4 2.5 - - - +
686A GLY 5.1 1.3 - - - -
687A THR* 3.7 24.9 - - - +
702A LYS* 4.5 23.3 - - + +
703A ARG* 1.3 75.3 - - - +
705A LEU* 1.3 65.8 + - - +
708A PHE* 3.9 31.0 - - + +
711A ILE* 4.6 13.0 - - + -
712A ALA* 4.0 22.9 - - - +
715A GLU* 4.6 8.1 - - - +
740A PHE* 3.4 13.3 - - - -
741A LEU* 2.9 40.5 + - + +
743A ILE* 5.1 5.6 - - + -
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Residues in contact with LEU 705 (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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685A SER 4.2 13.0 + - - +
686A GLY* 5.0 7.1 + - - +
704A MET* 1.3 76.7 - - - +
706A ILE* 1.3 66.1 + - - +
707A ASP* 4.2 9.0 - - + +
708A PHE* 3.0 51.5 + - + +
739A ARG 4.8 3.6 - - - +
740A PHE* 4.2 21.1 - - + -
741A LEU* 4.5 2.6 - - - +
682B TYR* 4.8 3.6 - - + -
686B GLY* 3.9 23.6 - - - +
688B VAL* 3.2 30.5 - - + -
703B ARG* 4.3 14.1 - - - +
705B LEU* 6.3 1.8 - - + -
740B PHE* 5.7 5.2 - - + -
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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