Contacts of the strand formed by residues 731 - 735 (chain A) in PDB entry 1N1M
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 GLN 731 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A GLU* 6.1 0.9 - - + +
700A TYR 2.9 17.3 + - - +
701A LEU* 3.6 17.6 - - + -
702A LEU* 3.0 23.4 + - - +
729A ASP* 5.1 4.6 + - - -
730A PHE* 1.3 85.5 + - - +
732A ALA* 1.3 62.4 + - - +
754A HIS* 5.2 3.1 + - - +
758A PHE* 4.1 20.0 - - + -
731B GLN* 2.7 31.5 + - - +
754B HIS* 3.6 24.0 - - - -
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Residues in contact with ALA 732 (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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701A LEU* 4.5 2.2 - - - -
702A LEU 3.4 7.0 - - - +
730A PHE* 4.2 9.3 + - + -
731A GLN* 1.3 77.4 - - - +
733A MET* 1.3 66.7 + - - +
754A HIS* 4.4 7.3 + - - -
731B GLN* 5.4 2.3 + - - +
732B ALA 3.0 35.8 + - - +
733B MET* 3.7 27.1 - - + -
734B TRP* 4.1 16.6 - - + -
754B HIS* 5.6 0.2 - - - -
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Residues in contact with MET 733 (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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702A LEU 3.1 4.7 + - - +
703A ILE* 3.3 38.6 - - + +
704A HIS 3.4 3.5 + - - -
732A ALA* 1.3 79.7 - - - +
734A TRP* 1.3 75.3 + - - +
735A TYR* 3.6 28.3 - - + +
750A HIS* 4.1 15.3 - - + -
754A HIS* 4.0 24.5 - - + +
720B SER* 5.9 0.2 - - - -
730B PHE* 3.0 48.7 - - + +
732B ALA* 3.9 22.9 - - + +
734B TRP* 3.8 5.8 - - - -
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Residues in contact with TRP 734 (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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704A HIS 3.5 11.2 - - - +
706A THR* 3.8 13.2 - - + -
713A PHE* 4.2 10.8 - - + -
733A MET* 1.3 91.2 - - - +
735A TYR* 1.3 68.2 + - - +
736A THR* 3.6 17.8 - - + +
702B LEU* 4.1 23.1 - - + -
704B HIS* 5.1 1.6 - - + -
713B PHE* 3.7 26.7 - + - -
716B SER* 3.8 26.5 - - - -
717B ALA* 4.1 5.3 - - - +
720B SER* 3.0 30.4 + - - -
732B ALA* 3.9 11.9 - - + -
733B MET 3.8 32.3 - - - -
734B TRP* 3.9 35.2 - + + -
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Residues in contact with TYR 735 (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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703A ILE* 3.7 25.4 - - + -
704A HIS 3.4 7.6 + - - -
705A GLY* 3.5 4.6 - - - -
706A THR* 2.9 22.9 + - - -
733A MET* 3.6 23.5 - - + +
734A TRP* 1.3 77.5 - - - +
736A THR* 1.3 66.4 + - - +
738A GLU* 3.3 24.0 + - + -
742A ILE* 4.2 14.4 - - + -
747A ALA* 4.3 15.3 - - + -
750A HIS* 2.6 45.1 + + + -
751A ILE* 3.0 32.1 - - + +
754A HIS* 4.4 3.1 - - - +
720B SER* 6.2 0.2 - - - -
724B VAL* 3.9 17.9 - - + -
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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