Contacts of the strand formed by residues 748 - 756 (chain B) in PDB entry 1N7J
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 TYR 748 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B LEU* 4.6 3.5 - - - +
698B LEU* 4.0 5.3 - - + +
701B ILE* 4.9 0.2 - - - +
702B THR* 2.8 49.0 + - + +
705B LEU* 3.9 20.5 - - + +
711B LEU* 3.4 39.1 - - + +
743B LEU* 3.0 34.3 + - + +
744B VAL* 3.7 20.5 + - - +
746B SER* 3.8 13.9 - - - -
747B GLY* 1.3 78.6 - - - +
749B LYS* 1.3 60.1 + - - +
750B VAL 3.7 2.3 + - - -
777B ALA* 3.6 24.2 - - + -
778B GLN 3.2 7.9 - - - -
779B LYS* 3.5 20.9 - - + -
780B VAL* 4.1 3.5 - - - +
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Residues in contact with LYS 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744B VAL* 5.9 0.2 - - - -
748B TYR* 1.3 72.3 - - - +
750B VAL* 1.3 64.4 + - - +
751B ARG* 3.1 30.1 + - + +
777B ALA* 4.4 0.4 - - - -
778B GLN* 2.8 41.5 + - + +
780B VAL* 4.0 10.9 - - + +
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Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B ARG* 4.1 41.1 - - + +
743B LEU* 3.7 39.5 - - + -
744B VAL* 4.4 10.6 - - + +
748B TYR 3.7 1.0 + - - +
749B LYS* 1.3 74.9 - - - +
751B ARG* 1.3 60.4 + - - +
752B ASP* 4.0 19.1 - - - +
753B LEU* 4.2 10.3 - - + -
776B TRP 4.1 3.4 - - - +
777B ALA* 4.4 2.7 - - + -
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Residues in contact with ARG 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569B GLU* 2.8 42.8 + - - -
710B HIS* 3.9 6.5 - - - -
749B LYS* 3.1 29.2 + - - +
750B VAL* 1.3 73.9 - - - +
752B ASP* 1.3 59.1 + - - +
776B TRP* 2.8 61.3 + - + +
778B GLN* 3.8 32.3 + - + +
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Residues in contact with ASP 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 4.5 7.3 + - - -
564B THR* 5.0 0.9 + - - -
750B VAL* 3.5 6.0 - - - +
751B ARG* 1.3 82.5 - - - +
753B LEU* 1.3 68.9 + - - +
754B ARG* 2.8 48.1 + - - +
774B PHE* 3.9 11.5 - - - -
775B ALA* 3.1 4.0 - - - +
776B TRP* 2.7 53.5 + - + +
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Residues in contact with LEU 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU* 4.4 0.2 - - - +
240A ARG* 4.3 4.2 + - - -
253A LEU 4.0 16.8 - - - +
736B GLU* 3.4 31.2 - - + +
739B VAL* 4.4 4.7 - - + -
740B ARG* 3.7 58.5 + - + +
743B LEU* 5.0 0.9 - - + -
750B VAL* 4.2 8.0 - - + +
752B ASP* 1.3 78.5 + - - +
754B ARG* 1.3 63.4 + - - +
773B PHE* 4.2 19.5 - - + -
774B PHE 3.2 16.8 - - - +
775B ALA* 3.5 18.2 - - + -
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Residues in contact with ARG 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU* 3.5 9.9 - - - +
237A GLU* 3.1 25.6 + - - +
240A ARG* 3.4 20.3 - - - +
556B TRP* 3.7 14.6 - - + -
559B ARG* 4.5 1.0 - - - +
560B CYS* 3.7 30.1 + - - +
563B GLN* 3.2 46.6 + - - +
564B THR* 4.6 8.3 + - - +
736B GLU* 4.7 1.3 - - - -
752B ASP* 2.8 32.9 + - - +
753B LEU* 1.3 78.6 - - - +
755B THR* 1.3 62.8 + - - +
773B PHE* 3.2 8.1 - - - +
774B PHE* 2.8 38.7 + - + +
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Residues in contact with THR 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLU* 2.6 28.8 + - - +
237A GLU* 5.1 0.5 - - - +
255A THR* 3.2 32.9 + - - +
257A ILE* 4.5 7.6 - - + -
556B TRP* 4.0 7.9 + - - -
717B LEU* 3.2 30.6 - - + +
736B GLU* 3.5 24.1 + - - +
754B ARG* 1.3 73.9 + - - +
756B TYR* 1.3 70.2 + - - +
757B ILE* 4.1 10.6 + - + +
772B VAL 3.4 2.9 - - - -
773B PHE* 4.6 0.5 - - - +
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Residues in contact with TYR 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B ASN 3.1 24.9 + - - -
552B GLY 3.8 11.9 - - - -
553B VAL* 3.3 38.6 + - + -
556B TRP* 3.6 44.6 - + + +
755B THR* 1.3 75.7 - - - +
757B ILE* 1.3 61.1 - - - +
758B MET* 3.2 24.9 + - - -
759B PRO* 3.1 19.9 - - + +
762B LEU* 3.3 11.6 - - - +
771B GLY* 2.8 5.7 - - - -
772B VAL* 2.8 43.7 + - + +
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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