Contacts of the helix formed by residues 587 - 592 (chain B) 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 GLY 587 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B GLY 3.1 16.4 - - - -
381B TYR* 4.2 8.7 - - - -
382B ARG* 6.0 0.2 - - - -
403B GLU* 3.2 17.0 + - - -
583B SER 5.0 0.2 - - - +
585B TYR 4.7 0.4 - - - +
586B GLN* 1.3 82.0 + - - +
588B ASP* 1.3 63.1 + - - -
589B LYS* 3.2 4.5 - - - -
590B ILE* 3.2 4.3 + - - +
591B MET* 3.0 26.5 + - - +
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Residues in contact with ASP 588 (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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349B SER* 5.4 0.9 + - - -
351B THR* 4.2 6.4 + - + +
376B SER* 3.1 29.2 + - - -
380B GLY* 2.7 25.2 + - - +
382B ARG* 2.8 34.0 + - - -
587B GLY* 1.3 70.4 - - - -
589B LYS* 1.3 65.7 + - - +
590B ILE 3.1 0.2 - - - -
591B MET* 3.8 9.3 - - - +
592B HIS* 2.9 51.1 + - - +
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Residues in contact with LYS 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLU 5.7 5.1 + - - +
380B GLY* 5.3 2.0 - - - -
381B TYR* 6.1 2.7 - - + +
522B THR* 6.2 3.6 - - - +
581B ARG* 5.7 0.2 - - - +
586B GLN 5.7 1.1 - - - +
587B GLY* 3.2 2.4 - - - -
588B ASP* 1.3 78.9 - - - +
590B ILE* 1.3 66.3 + - + +
592B HIS 4.6 0.2 - - - -
593B ALA* 3.8 15.6 + - - +
780B NAG 5.9 3.3 + - - -
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Residues in contact with ILE 590 (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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522B THR* 4.5 13.5 - - - +
523B LYS 4.7 5.8 - - - +
524B PHE* 4.4 18.6 - - + -
580B GLY 4.0 8.3 - - - +
581B ARG* 3.9 6.7 - - + -
582B GLY 2.8 22.6 + - - +
583B SER* 3.4 29.8 - - - +
586B GLN* 3.7 40.6 - - + +
587B GLY 3.2 7.0 + - - +
589B LYS* 1.3 85.7 - - + +
591B MET* 1.3 64.3 + - - +
593B ALA* 3.4 11.9 + - - +
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Residues in contact with MET 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TRP* 3.7 35.7 - - + +
356B ARG* 4.0 9.2 - - - -
382B ARG* 3.1 38.1 - - - +
550B PRO* 5.5 0.2 - - - +
551B CYS* 3.3 35.4 + - + -
582B GLY* 3.5 22.9 - - - +
583B SER 3.5 14.1 - - - +
584B GLY* 4.5 5.6 - - - -
585B TYR 5.3 1.3 - - - +
587B GLY 3.0 16.8 + - - +
588B ASP* 4.0 4.9 - - - +
590B ILE* 1.3 79.5 - - - +
592B HIS* 1.3 72.1 + - + +
593B ALA 3.4 2.9 + - - -
594B ILE* 4.0 4.5 - - - +
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Residues in contact with HIS 592 (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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349B SER* 3.8 11.0 - - - -
351B THR* 2.5 43.0 + - - +
352B GLY* 3.3 20.2 + - - -
353B TRP* 3.5 45.0 + + - -
382B ARG* 4.0 3.6 + - - -
588B ASP* 2.9 39.4 + - + +
589B LYS 4.6 0.4 - - - -
591B MET* 1.3 91.4 - - + +
593B ALA* 1.3 65.4 + - - +
594B ILE 3.2 3.1 - - - -
595B ASN* 3.1 18.2 + - + +
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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