Contacts of the strand formed by residues 726 - 734 (chain N) in PDB entry 1M8V
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 GLU 726 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147H MET* 5.9 1.7 - - - +
155H LYS* 4.5 17.8 + - - +
157H TYR* 5.4 2.5 + - - -
718N LEU* 3.5 27.8 - - + +
719N VAL 3.0 20.4 - - - +
720N ILE* 4.1 15.6 - - - +
721N LEU 4.5 0.7 - - - +
724N GLY 5.0 3.6 - - - +
725N PHE* 1.3 86.1 - - - +
727N PHE* 1.3 61.2 + - - +
728N ARG* 4.6 4.3 + - - -
747N MET* 3.6 1.7 - - - +
748N ILE* 2.7 56.5 + - + +
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Residues in contact with PHE 727 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620M ILE* 5.0 3.8 - - + -
668M LEU* 5.2 4.7 - - + -
669M ALA* 5.3 1.8 - - + -
717N VAL 4.0 0.5 - - - +
718N LEU* 3.7 3.3 - - - +
719N VAL* 2.8 40.0 + - + +
721N LEU* 3.7 30.3 - - + -
725N PHE* 3.8 8.3 - + - -
726N GLU* 1.3 77.3 - - - +
728N ARG* 1.3 62.4 + - - +
742N LEU* 4.1 16.6 - - + -
745N ALA* 4.7 5.8 - - + -
746N GLU 3.3 5.6 - - - -
747N MET* 3.2 41.5 - - + -
748N ILE* 5.5 0.7 - - - -
757N TYR* 3.4 31.2 - + - -
760N ILE* 3.5 24.5 - - + -
762N ILE* 4.0 20.6 - - + -
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Residues in contact with ARG 728 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716N ASP* 5.7 6.7 - - + -
717N VAL 3.6 9.9 - - - +
718N LEU* 3.6 41.9 - - + +
726N GLU* 4.6 4.8 + - - -
727N PHE* 1.3 75.2 - - - +
729N GLY* 1.3 62.1 + - - +
742N LEU* 4.5 2.9 - - - -
744N ASP 3.9 0.9 - - - +
745N ALA* 3.1 3.7 - - - +
746N GLU* 2.7 47.7 + - + +
748N ILE* 3.9 27.9 - - + +
773N THR 4.2 16.5 + - - +
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Residues in contact with GLY 729 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716N ASP* 3.3 9.5 - - - -
717N VAL* 2.8 33.7 + - - +
728N ARG* 1.3 78.7 - - - +
730N ARG* 1.3 62.9 + - - -
731N LEU 3.7 0.5 + - - -
742N LEU* 4.4 10.1 - - - +
743N ALA 3.8 2.2 - - - -
744N ASP 3.5 15.3 - - - -
745N ALA* 4.2 2.7 - - - -
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Residues in contact with ARG 730 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714N ASP* 3.5 44.6 + - - +
715N LYS 3.4 4.0 - - - +
716N ASP* 3.3 15.1 + - - +
729N GLY* 1.3 70.8 - - - -
731N LEU* 1.3 60.2 + - - +
732N ILE* 3.2 29.7 + - + +
742N LEU* 3.1 5.8 - - - -
743N ALA* 2.8 46.3 + - - +
744N ASP* 2.6 39.5 + - + +
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Residues in contact with LEU 731 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709N ILE* 3.2 39.9 - - + +
712N SER* 3.7 24.7 - - - +
713N LEU* 3.4 9.2 - - + +
714N ASP* 2.6 31.2 + - - -
715N LYS 2.8 10.6 + - - +
717N VAL* 3.9 16.4 - - + -
729N GLY 3.7 2.4 + - - -
730N ARG* 1.3 70.0 - - - +
732N ILE* 1.3 56.4 + - - +
733N GLY 3.2 29.2 - - - +
734N TYR* 4.8 0.9 - - + -
740N VAL* 4.0 18.8 - - + -
741N VAL 3.4 9.6 - - - +
742N LEU* 3.8 7.4 - - + -
770N ILE* 6.0 4.3 - - + -
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Residues in contact with ILE 732 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603M GLU* 3.1 52.8 + - + +
713N LEU* 3.8 6.5 - - - +
714N ASP* 4.8 9.9 - - - +
730N ARG* 3.5 39.7 - - - +
731N LEU* 1.3 76.0 - - - +
733N GLY* 1.3 55.3 + - - -
741N VAL* 2.8 40.0 + - + +
742N LEU 4.4 0.7 - - - -
743N ALA* 3.9 16.6 - - + +
759N LYS* 4.0 12.3 - - + -
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Residues in contact with GLY 733 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603M GLU 3.5 13.0 - - - -
605M PRO* 4.2 2.5 - - - -
713N LEU* 3.3 10.7 - - - +
731N LEU* 3.2 8.4 - - - +
732N ILE* 1.3 79.9 - - - +
734N TYR* 1.3 68.8 + - - +
741N VAL* 2.8 24.7 + - - -
1U U 3.5 13.2 - - - -
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Residues in contact with TYR 734 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604M ARG* 3.9 3.6 - - - +
605M PRO* 3.4 18.5 - - - +
706N LEU* 4.4 18.7 + - + -
709N ILE* 3.6 21.8 - - + -
710N HIS* 2.8 53.5 + - + +
713N LEU* 4.2 11.7 - - + -
731N LEU* 4.8 1.6 - - + -
733N GLY* 1.3 78.8 - - - +
735N ASP* 1.3 76.8 + - - +
736N ILE* 6.2 0.4 - - + -
738N LEU* 5.5 1.1 - - + -
739N ASN 3.3 17.0 - - - +
740N VAL* 4.1 9.4 - - + -
1U U 2.7 73.5 + + - +
2U U 4.3 3.6 + - - -
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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