Contacts of the helix formed by residues 361 - 374 (chain B) in PDB entry 2IHU
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 ILE 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B TYR* 3.7 66.1 + - + +
283B THR* 3.6 35.4 - - + +
284B MET* 4.3 10.3 - - - -
359B HIS* 3.7 8.4 + - - +
360B ASP* 1.3 76.4 + - - +
362B GLU* 1.3 66.2 + - - +
363B PRO* 3.3 3.6 - - - -
364B LEU* 3.0 21.6 + - + +
365B ARG* 3.0 42.4 + - + +
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Residues in contact with GLU 362 (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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360B ASP* 2.9 21.6 + - - +
361B ILE* 1.3 78.5 + - - +
363B PRO* 1.4 59.1 - - + +
365B ARG* 2.9 45.8 + - - +
366B ALA* 2.8 32.3 + - - +
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Residues in contact with PRO 363 (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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278B PHE* 3.3 26.9 - - + -
283B THR* 4.8 7.0 - - + +
360B ASP* 3.9 13.9 - - - +
361B ILE* 3.3 7.4 - - - -
362B GLU* 1.4 92.9 - - + +
364B LEU* 1.3 55.1 + - - +
366B ALA* 3.6 7.7 + - + +
367B ARG 3.2 19.8 + - - -
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Residues in contact with LEU 364 (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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265B TYR 5.3 0.2 - - - +
272B MET* 4.7 2.2 - - + -
276B LEU* 3.8 18.8 - - + -
278B PHE* 3.6 16.4 - - + -
280B ALA* 3.7 40.2 - - + +
283B THR* 3.8 16.5 - - + +
284B MET* 3.5 35.4 - - + -
361B ILE* 3.0 17.7 + - + +
363B PRO* 1.3 76.2 - - - +
365B ARG* 1.3 61.3 + - + +
367B ARG* 3.2 3.0 + - + +
368B ILE* 3.0 41.3 + - + +
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Residues in contact with ARG 365 (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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261B HIS 4.1 3.8 + - - -
262B GLU* 3.1 32.7 + - - +
264B ASN 3.2 24.9 + - - -
265B TYR* 3.6 14.1 + - - -
358B ARG* 5.4 5.7 - - - +
361B ILE* 3.0 34.3 + - + +
362B GLU* 2.9 44.0 + - - +
364B LEU* 1.3 76.0 - - + +
366B ALA* 1.3 58.1 + - - +
368B ILE* 3.5 10.3 + - + +
369B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 366 (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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362B GLU 2.8 21.0 + - - +
363B PRO* 3.6 9.0 - - + +
365B ARG* 1.3 73.6 - - - +
367B ARG* 1.3 56.2 + - - +
369B ALA* 3.4 6.5 + - - +
370B GLU* 3.0 30.5 + - - +
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Residues in contact with ARG 367 (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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276B LEU* 2.8 37.8 + - + +
277B ASN* 4.0 18.5 + - - +
278B PHE* 3.6 34.6 - - + -
363B PRO 3.2 11.7 + - - +
364B LEU* 3.2 9.2 + - + +
366B ALA* 1.3 77.1 - - - +
368B ILE* 1.3 64.8 + - - +
370B GLU* 2.9 37.7 + - - +
371B PHE* 3.2 39.6 + - - -
603B GOL 3.7 15.2 + - - -
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Residues in contact with ILE 368 (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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272B MET* 5.7 2.0 - - + -
276B LEU* 4.2 22.9 - - + -
284B MET* 6.2 0.7 - - + -
364B LEU* 3.0 40.5 + - + +
365B ARG* 3.9 8.5 - - + +
367B ARG* 1.3 74.4 - - - +
369B ALA* 1.3 63.2 + - - +
371B PHE* 3.3 5.8 + - - +
372B LEU* 3.1 32.1 + - + +
419B LEU* 4.5 20.4 - - + +
420B PHE* 3.9 24.9 - - + -
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Residues in contact with ALA 369 (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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365B ARG 2.9 19.4 + - - +
366B ALA* 3.7 6.7 - - - +
367B ARG 3.3 0.2 - - - -
368B ILE* 1.3 77.7 - - - +
370B GLU* 1.3 57.0 + - - +
372B LEU* 3.5 10.3 + - - +
373B ALA* 3.1 30.5 + - - +
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Residues in contact with GLU 370 (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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366B ALA 3.0 16.4 + - - +
367B ARG* 2.9 42.7 + - - +
368B ILE 3.2 0.2 - - - -
369B ALA* 1.3 75.6 - - - +
371B PHE* 1.3 63.7 + - - +
373B ALA* 3.5 5.3 + - - +
374B ASP* 3.2 17.3 + - - -
603B GOL 3.7 20.1 + - - +
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Residues in contact with PHE 371 (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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275B ILE* 3.3 31.6 - - + -
276B LEU* 3.8 16.6 - - + -
367B ARG* 3.2 44.0 + - - -
368B ILE 3.4 9.0 - - - +
370B GLU* 1.3 78.9 - - - +
372B LEU* 1.3 64.2 + - - +
374B ASP* 3.1 12.5 + - - +
385B HIS* 3.1 59.0 - + + -
416B TYR* 4.6 3.8 - + - -
420B PHE* 3.7 25.6 - + + -
603B GOL 3.5 30.7 - - - -
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Residues in contact with LEU 372 (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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368B ILE* 3.1 26.3 + - + +
369B ALA* 3.8 7.9 - - - +
370B GLU 3.4 0.2 - - - -
371B PHE* 1.3 79.1 - - - +
373B ALA* 1.3 57.2 + - - +
385B HIS* 3.9 9.6 - - + +
389B ASP* 2.9 51.1 - - + +
392B ASN* 4.3 5.6 - - - +
420B PHE* 3.7 49.4 - - + +
536B ARG* 2.9 19.1 + - - -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ALA 3.1 18.4 + - - +
370B GLU* 3.9 5.4 - - - +
371B PHE 3.2 0.4 - - - -
372B LEU* 1.3 75.4 - - - +
374B ASP* 1.3 67.4 + - - +
375B PRO* 2.9 12.9 - - - +
389B ASP* 5.0 1.6 - - - -
536B ARG* 3.6 5.3 + - - +
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Residues in contact with ASP 374 (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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370B GLU 3.2 8.0 + - - +
371B PHE 3.1 17.5 + - - +
372B LEU 3.4 0.8 - - - -
373B ALA* 1.3 70.3 - - - +
375B PRO* 1.4 71.4 - - - +
376B GLU* 3.2 14.4 + - - +
378B TYR* 2.7 30.4 + - - -
385B HIS* 2.9 25.0 + - + +
386B GLN* 3.2 12.8 + - - +
536B ARG* 2.8 29.3 + - - +
603B GOL 3.5 22.8 - - - -
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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