Contacts of the helix formed by residues 400 - 409 (chain A) in PDB entry 1IGN
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A HIS* 5.2 1.1 - - - -
388A TYR* 3.4 31.8 - - - +
389A ASP* 3.8 10.1 + - - +
392A SER* 3.8 8.1 + - - -
399A THR* 1.3 72.6 - - - +
401A ASN* 1.3 56.9 + - - +
404A ARG* 2.8 34.3 + - - +
592A TYR* 3.5 13.0 + - - -
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Residues in contact with ASN 401 (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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385A HIS* 5.1 3.3 + - - -
399A THR 3.1 0.4 - - - -
400A GLY* 1.3 76.1 - - - +
402A SER* 1.3 61.1 + - - +
404A ARG* 4.0 4.6 - - - +
405A HIS* 3.2 24.4 + - - +
590A GLY 3.9 0.5 - - - +
591A ASN* 3.3 14.5 + - - -
592A TYR* 3.0 38.3 + - - +
593A ASN* 3.2 4.0 - - - +
6C C 4.0 3.4 - - + -
7C A 2.9 50.7 + - + +
8C C 2.8 32.6 + - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PHE* 3.4 7.0 - - - -
398A HIS* 3.4 3.5 - - - +
399A THR* 3.0 31.0 + - - -
401A ASN* 1.3 76.7 - - - +
403A ILE* 1.3 60.1 + - - +
405A HIS* 3.9 0.9 - - - +
406A ARG* 2.8 32.2 + - - +
5C A 4.0 4.2 - - - +
6C C 2.8 58.1 + - - +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PHE* 4.1 12.3 - - + -
371A ILE* 3.9 20.3 - - + +
388A TYR* 3.7 24.0 - - + +
391A ILE* 3.8 12.1 - - + -
392A SER* 3.5 28.5 - - - +
395A VAL* 3.5 29.6 - - + -
398A HIS* 3.8 17.5 - - + -
399A THR 2.8 18.9 + - - +
400A GLY 3.8 3.1 - - - +
402A SER* 1.3 74.9 - - - +
404A ARG* 1.3 59.0 + - - +
406A ARG* 3.3 2.7 + - - +
407A PHE* 2.8 29.8 + - - +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A THR* 3.4 24.2 + - - +
384A THR 3.0 21.4 + - - -
385A HIS* 3.4 30.5 + - - +
388A TYR* 3.7 26.3 - - + +
400A GLY 2.8 19.3 + - - +
401A ASN* 4.0 4.3 - - - +
403A ILE* 1.3 74.3 - - - +
405A HIS* 1.3 55.1 + - - +
407A PHE* 3.1 3.1 + - - +
408A ARG* 2.7 57.2 + - + +
8C C 5.9 0.4 - - - +
30D G 3.7 3.6 - - - -
31D G 2.6 30.2 + - - -
32D G 3.0 38.4 + - - +
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Residues in contact with HIS 405 (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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401A ASN 3.2 17.1 + - - +
402A SER 3.9 1.3 - - - +
404A ARG* 1.3 75.6 - - - +
406A ARG* 1.3 68.6 + - - +
408A ARG* 4.3 8.9 + - - +
409A VAL* 2.9 54.8 + - + +
410A TYR* 4.2 15.7 + + - -
4C C 6.1 0.8 - - - -
5C A 4.2 14.9 + + - -
6C C 3.2 41.0 + + + +
7C A 4.6 4.5 - - - +
33D T 4.0 19.7 + + + +
34D G 4.3 4.9 - - - -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PHE* 3.6 39.2 + - + +
368A ASP* 2.8 44.0 + - - +
371A ILE* 4.5 1.1 - - + -
402A SER 2.8 24.2 + - - +
403A ILE* 3.5 4.0 - - - +
405A HIS* 1.3 74.7 - - - +
407A PHE* 1.3 58.5 + - - +
410A TYR* 2.9 62.2 + - - +
411A LEU* 2.9 17.0 + - + +
414A ARG* 4.7 4.9 - - - +
4C C 4.4 6.1 - - - -
5C A 2.9 30.8 + - - +
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Residues in contact with PHE 407 (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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371A ILE* 4.1 19.7 - - + -
372A LEU* 3.9 20.9 - - + -
375A VAL* 3.7 27.8 - - + -
382A ARG* 4.4 10.3 - - + -
388A TYR* 3.3 31.2 - + + -
403A ILE 2.8 21.4 + - - +
404A ARG 3.4 3.4 - - - +
406A ARG* 1.3 73.3 - - - +
408A ARG* 1.3 69.2 + - + +
411A LEU* 2.9 24.3 + - + +
412A SER* 2.7 46.6 + - - -
415A LEU* 4.1 18.2 - - + -
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Residues in contact with ARG 408 (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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382A ARG 6.0 1.8 - - - +
383A THR* 6.1 4.3 - - + -
388A TYR* 6.2 0.2 - - + -
404A ARG* 2.7 59.0 + - + +
405A HIS* 3.8 7.8 + - - +
407A PHE* 1.3 81.2 - - + +
409A VAL* 1.3 75.9 + - + +
412A SER* 2.6 26.7 + - - -
31D G 4.0 17.3 - - - +
32D G 3.4 41.6 + - - -
33D T 3.7 19.0 - - - +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A HIS* 2.9 41.8 + - + +
408A ARG* 1.3 100.0 - - + +
410A TYR* 1.3 85.0 + - + +
412A SER* 4.7 1.5 + - - -
413A LYS* 4.1 14.9 - - - +
33D T 5.7 1.3 - - + -
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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