Contacts of the helix formed by residues 588 - 593 (chain A) in PDB entry 1N35
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 ALA 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A GLN* 6.0 7.2 - - + +
524A ARG* 5.4 4.6 - - - +
587A SER* 1.3 78.8 - - - +
589A CYS* 1.3 65.5 + - - +
590A ASP 3.4 2.5 - - - -
591A ALA* 3.1 17.0 + - + +
592A SER* 2.9 24.9 + - - +
1291A CH1 3.6 17.0 + - - -
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Residues in contact with CYS 589 (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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586A ILE* 3.8 13.4 + - + +
587A SER 3.1 3.7 - - - -
588A ALA* 1.3 75.5 - - - +
590A ASP* 1.3 59.6 + - - +
592A SER* 2.9 27.4 + - - -
593A ILE* 3.3 18.4 + - - +
691A HIS* 3.4 36.3 - - + -
734A ASP* 3.5 42.2 - - + +
769A TRP* 5.9 3.6 - - - -
1291A CH1 4.0 11.4 + - - +
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Residues in contact with ASP 590 (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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588A ALA 3.4 0.4 - - - -
589A CYS* 1.3 78.3 - - - +
591A ALA* 1.3 62.1 + - - +
592A SER 3.3 0.7 + - - -
593A ILE 3.4 5.9 + - - +
679A THR* 3.6 9.0 - - + -
680A PHE* 2.8 50.2 + - - +
682A SER* 3.4 9.1 + - - -
687A THR* 3.9 5.1 - - - +
691A HIS* 2.8 33.9 + - - -
1291A CH1 3.1 41.5 + - - +
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Residues in contact with ALA 591 (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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388A GLU 4.6 6.7 - - - +
391A GLN* 3.8 19.5 - - + +
393A PRO* 2.7 33.2 - - + +
588A ALA* 3.1 20.0 + - + +
590A ASP* 1.3 78.3 - - - +
592A SER* 1.3 51.1 + - - +
593A ILE 3.4 0.2 - - - -
594A THR* 3.3 10.1 - - - +
678A THR* 5.4 0.2 + - - -
679A THR* 3.5 27.9 - - + +
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Residues in contact with SER 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PRO* 3.3 16.7 - - - +
395A ILE* 5.7 1.0 - - - +
586A ILE* 5.4 0.7 - - - -
587A SER 3.9 7.2 + - - -
588A ALA* 2.9 17.2 + - - +
589A CYS* 2.9 14.2 + - - -
591A ALA* 1.3 79.3 - - - +
593A ILE* 1.3 60.2 + - - +
594A THR* 3.4 6.7 + - - +
598A PHE* 3.7 15.6 - - - -
767A PHE 4.7 2.3 - - - +
768A GLY 3.0 16.9 + - - -
769A TRP* 3.5 26.4 + - - -
770A LYS 5.1 0.2 + - - -
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Residues in contact with ILE 593 (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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589A CYS* 3.3 16.4 + - - +
590A ASP 3.4 5.5 + - - +
591A ALA 3.4 1.0 - - - -
592A SER* 1.3 74.5 - - - +
594A THR* 1.3 61.7 + - - +
598A PHE* 4.0 17.9 - - + -
599A LEU* 3.7 35.4 - - + +
678A THR 4.2 1.9 - - - +
680A PHE* 3.7 21.5 + - + +
690A GLU* 3.9 15.7 - - - +
691A HIS* 3.6 25.6 - - + +
694A ASN* 4.2 9.2 - - + +
769A TRP* 3.7 36.8 - - + +
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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