Contacts of the helix formed by residues 428 - 438 (chain B) in PDB entry 2IHM
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 GLN 428 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B THR* 3.7 12.7 + - - +
425B PRO* 2.5 40.5 + - + +
427B SER* 1.3 79.5 - - - +
429B PHE* 1.3 63.7 + - - +
430B PRO* 2.9 7.5 - - - -
431B PHE* 3.1 17.1 + - + -
432B ALA* 3.3 8.0 + - - +
460B SER 5.2 0.2 - - - +
461B HIS* 3.5 56.2 + - - +
462B GLY* 5.5 0.4 - - - -
464B PHE* 5.6 4.4 - - - -
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Residues in contact with PHE 429 (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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314B THR* 5.0 4.0 - - + -
316B THR* 3.3 32.8 - - + -
334B LEU* 3.8 25.6 - - + -
336B THR* 3.6 31.6 - - + -
424B THR* 3.8 18.6 - - + -
425B PRO 3.3 4.9 + - - -
426B SER* 3.3 16.1 + - - +
428B GLN* 1.3 76.0 - - - +
430B PRO* 1.3 67.2 - - + +
432B ALA* 3.2 2.9 + - - +
433B LEU* 2.8 50.8 + - + +
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Residues in contact with PRO 430 (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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426B SER 4.2 5.2 - - - +
427B SER 4.3 1.6 - - - +
428B GLN* 3.2 7.4 - - - -
429B PHE* 1.3 98.3 - - + +
431B PHE* 1.3 63.0 + - + +
433B LEU* 3.4 6.1 + - + +
434B LEU* 3.1 23.7 + - - +
474B ALA* 3.3 35.4 - - + +
475B THR 2.9 29.2 - - - +
476B SER* 3.9 18.2 - - - +
477B GLU* 4.3 5.7 - - + +
480B VAL* 4.5 4.8 - - + +
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B SER 5.6 2.2 - - - -
428B GLN* 3.1 14.1 + - + +
430B PRO* 1.3 76.7 - - + +
432B ALA* 1.3 57.5 + - - +
434B LEU* 3.7 7.4 + - + +
435B GLY* 3.1 20.3 + - - -
458B LEU* 4.0 14.0 - - + +
459B ASN 3.9 4.0 - - - +
460B SER* 3.2 15.6 - - - +
461B HIS 3.2 26.7 - - - +
462B GLY* 3.2 15.0 - - - +
463B LEU* 3.1 34.8 - - + -
472B PHE 4.6 14.4 - - - -
473B HIS* 4.8 2.0 - - - -
474B ALA* 3.7 30.3 - - + -
480B VAL* 4.2 21.3 - - + -
483B LEU* 5.0 5.8 - - + -
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Residues in contact with ALA 432 (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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334B LEU* 3.8 19.5 - - + -
422B VAL* 5.9 0.9 - - + -
424B THR* 3.8 21.8 - - - +
428B GLN 3.3 7.9 + - - +
429B PHE 3.2 8.4 + - - +
431B PHE* 1.3 76.6 - - - +
433B LEU* 1.3 60.8 + - - +
435B GLY 3.3 0.3 + - - -
436B TRP* 2.9 41.6 + - + +
460B SER* 3.1 18.1 + - - +
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Residues in contact with LEU 433 (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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316B THR* 3.9 14.6 - - + -
318B THR* 3.4 28.7 - - + -
322B ARG* 3.5 32.8 - - - +
334B LEU* 3.6 10.3 - - + +
429B PHE* 2.8 40.5 + - + +
430B PRO* 3.8 5.2 - - + +
432B ALA* 1.3 72.7 - - - +
434B LEU* 1.3 60.3 + - - +
436B TRP 4.0 0.3 - - - -
437B THR* 2.4 38.6 + - - +
477B GLU* 3.6 19.3 - - + +
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Residues in contact with LEU 434 (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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430B PRO 3.1 16.7 + - - +
431B PHE* 3.8 6.7 - - - +
433B LEU* 1.3 79.6 - - - +
435B GLY* 1.3 53.7 + - - +
436B TRP 3.5 0.2 + - - -
437B THR* 3.6 7.8 + - - -
438B GLY 4.0 1.2 + - - +
442B PHE* 4.4 3.5 - - + -
443B GLU* 2.7 23.6 - - - +
446B LEU* 3.5 31.4 - - + -
458B LEU* 4.6 10.5 - - + -
477B GLU* 3.5 13.4 + - + +
480B VAL* 3.8 31.6 - - + -
481B PHE* 3.5 33.7 - - + -
494B ARG* 4.0 16.8 + - - +
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Residues in contact with GLY 435 (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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638A D3T 3.3 17.2 - - - +
431B PHE 3.1 12.9 + - - -
432B ALA 3.3 2.6 + - - -
434B LEU* 1.3 81.7 - - - +
436B TRP* 1.3 62.1 + - - +
443B GLU* 3.2 30.4 - - - +
447B ARG* 4.4 13.1 + - - -
459B ASN 5.9 0.2 - - - -
460B SER* 4.9 3.6 - - - -
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Residues in contact with TRP 436 (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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638A D3T 3.3 25.6 - - - +
318B THR* 3.5 18.7 + - + +
319B GLY* 2.9 25.5 + - - -
332B ASP* 4.1 20.4 - - + -
333B PHE 5.7 1.1 - - - -
334B LEU* 5.1 4.7 - - + -
389B ARG* 3.8 28.9 - - + +
391B PHE* 3.8 15.7 - + - -
420B ASP* 4.2 6.1 - - + -
422B VAL* 3.5 46.5 - - + +
432B ALA* 2.9 29.8 + - + +
435B GLY* 1.3 74.4 - - - +
437B THR* 1.3 59.1 + - - +
438B GLY 3.5 1.1 - - - -
460B SER* 4.3 19.3 + - - -
6Q T 3.2 36.6 - - - -
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Residues in contact with THR 437 (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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638A D3T 4.0 1.3 - - - -
318B THR* 4.4 0.5 - - - +
319B GLY 3.1 16.9 - - - +
322B ARG* 3.1 29.6 + - + +
323B ARG* 2.7 46.2 + - + +
433B LEU* 2.4 30.8 + - - +
434B LEU 3.6 2.4 + - - -
435B GLY 3.4 0.8 - - - -
436B TRP* 1.3 79.1 - - - +
438B GLY* 1.3 54.3 + - - +
491B PRO* 4.1 7.4 - - + -
494B ARG* 3.7 24.0 - - - +
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Residues in contact with GLY 438 (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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638A D3T 3.5 13.0 - - - +
323B ARG* 3.6 3.9 - - - -
436B TRP 3.5 2.0 - - - -
437B THR* 1.3 82.2 - - - +
439B SER* 1.3 69.8 + - - -
442B PHE* 3.5 11.0 - - - -
443B GLU* 3.2 17.6 + - - +
494B ARG* 3.5 24.6 - - - +
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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