Contacts of the helix formed by residues 400 - 409 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B HIS 5.3 1.6 - - - -
388B TYR* 3.4 31.6 - - - +
389B ASP* 3.7 11.3 + - - +
392B SER* 4.1 5.9 + - - -
399B THR* 1.3 73.4 - - - +
401B ASN* 1.3 56.8 + - - +
404B ARG* 2.9 33.2 + - - +
592B TYR* 3.3 14.7 + - - -
593B ASN 5.1 0.8 + - - -
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Residues in contact with ASN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B HIS* 5.0 4.2 + - - -
399B THR 3.1 0.2 - - - -
400B GLY* 1.3 75.6 - - - +
402B SER* 1.3 57.8 + - - +
404B ARG* 3.3 7.2 + - - +
405B HIS* 3.0 29.7 + - - +
590B GLY 4.0 0.9 - - - +
591B ASN* 3.0 23.2 + - - -
592B TYR* 3.0 35.7 + - - +
593B ASN* 3.3 1.6 - - - +
6E C 4.0 1.5 - - + -
7E A 3.0 47.3 + - + +
8E C 3.0 28.0 + - - +
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Residues in contact with SER 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 3.4 8.1 - - - -
398B HIS* 3.3 2.6 - - - +
399B THR* 2.9 30.2 + - - -
401B ASN* 1.3 75.7 - - - +
403B ILE* 1.3 56.5 + - - +
405B HIS* 3.3 1.3 + - - +
406B ARG* 2.7 36.0 + - - +
5E A 3.9 10.1 - - - -
6E C 3.0 49.7 + - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 3.9 10.8 - - + -
371B ILE* 3.7 28.5 - - + +
388B TYR* 3.6 19.5 - - + +
391B ILE* 3.9 10.8 - - + -
392B SER* 3.5 39.9 - - - +
395B VAL* 3.5 17.3 - - + -
398B HIS* 3.6 17.5 - - + -
399B THR 2.9 22.5 + - - +
400B GLY 3.8 2.5 - - - +
402B SER* 1.3 74.9 + - - +
404B ARG* 1.3 57.7 + - - +
406B ARG* 3.3 2.3 + - - +
407B PHE* 2.9 28.6 + - - +
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B THR* 3.2 27.3 + - - +
384B THR 2.9 20.2 + - - -
385B HIS* 3.3 36.3 + - - +
388B TYR* 3.7 28.5 - - + +
400B GLY 2.9 20.5 + - - +
401B ASN* 3.6 6.3 - - - +
403B ILE* 1.3 76.8 - - - +
405B HIS* 1.3 57.0 + - - +
407B PHE* 3.4 2.9 + - - +
408B ARG* 2.9 51.3 + - + +
8E C 6.0 0.4 - - - +
30F G 3.5 7.1 + - - -
31F G 2.8 25.5 + - - -
32F G 3.3 32.6 + - - +
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Residues in contact with HIS 405 (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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401B ASN 3.0 16.8 + - - +
402B SER 3.8 1.8 - - - +
404B ARG* 1.3 75.1 - - - +
406B ARG* 1.3 68.6 + - - +
408B ARG* 4.5 9.8 + - - +
409B VAL* 3.0 54.0 + - + +
410B TYR* 5.0 8.1 - + - -
4E C 6.1 1.4 - - - -
5E A 4.2 15.2 + + - -
6E C 3.2 44.8 + + + +
7E A 4.2 4.2 + - - +
33F T 4.1 20.5 + - + +
34F G 4.5 4.0 - - - -
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Residues in contact with ARG 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 3.5 49.0 + - + +
368B ASP* 2.8 39.4 + - - +
371B ILE* 4.6 1.1 - - + -
402B SER 2.7 22.8 + - - +
403B ILE 3.4 5.4 - - - +
405B HIS* 1.3 75.8 - - - +
407B PHE* 1.3 62.7 + - - +
410B TYR* 3.1 50.3 + - - +
411B LEU* 3.2 21.2 + - + +
414B ARG* 5.0 1.6 - - - +
4E C 4.1 4.6 + - - -
5E A 2.7 36.8 + - - -
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Residues in contact with PHE 407 (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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371B ILE* 4.1 10.1 - - + -
372B LEU* 3.9 23.1 - - + -
375B VAL* 3.7 31.9 - - + -
382B ARG* 4.4 11.4 - - + -
388B TYR* 3.2 35.0 - + + -
403B ILE 2.9 16.8 + - - +
404B ARG 3.7 3.4 - - - +
406B ARG* 1.3 78.9 - - - +
408B ARG* 1.3 71.5 + - + +
411B LEU* 3.2 17.3 + - + +
412B SER* 2.8 54.3 + - - -
415B LEU* 4.1 15.7 - - + -
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ARG 5.9 2.5 - - - +
383B THR* 5.9 6.3 - - - +
388B TYR* 6.1 0.2 - - + -
404B ARG* 2.9 50.3 + - + +
405B HIS* 3.4 9.1 + - - +
407B PHE* 1.3 85.8 - - + +
409B VAL* 1.3 71.3 + - + +
412B SER* 2.6 25.0 + - - -
31F G 4.4 11.3 - - - +
32F G 3.3 52.4 + - - -
33F T 3.8 16.6 + - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B HIS* 3.0 48.5 + - + +
408B ARG* 1.3 89.7 - - + +
410B TYR* 1.3 84.6 + - + +
412B SER* 4.8 0.4 - - - -
413B LYS* 3.4 20.4 - - - +
33F T 6.3 0.2 - - + -
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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
------------------------------------------------------------
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