Contacts of the helix formed by residues 439 - 455 (chain A) 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 SER 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A ARG* 3.6 27.7 - - - +
438A GLY* 1.3 74.3 + - - -
440A GLN* 1.3 64.6 + - - +
441A PHE 3.6 0.4 + - - -
442A PHE* 2.8 23.2 + - - +
443A GLU* 2.9 11.3 + - - +
494A ARG 3.1 22.6 + - - -
495A ASN* 4.4 1.8 - - - -
496A ALA 2.6 30.3 + - - -
538A D3T 4.8 0.7 - - - -
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLY* 4.0 0.6 - - - -
439A SER* 1.3 75.1 - - - +
441A PHE* 1.3 66.9 + - - +
443A GLU* 3.1 12.9 + - - +
444A ARG* 3.3 38.8 + - - +
538A D3T 3.5 69.8 + - + +
6P T 5.9 0.6 - - - +
5T A 4.5 5.9 - - - +
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.1 1.6 - - + -
177A LEU* 4.0 23.1 - - + -
180A SER* 3.9 25.6 - - - -
181A ARG* 3.5 31.0 - - + -
184A SER* 3.6 21.8 - - - -
439A SER* 3.2 1.6 + - - -
440A GLN* 1.3 85.6 - - - +
442A PHE* 1.3 61.7 + - - +
444A ARG* 3.5 15.2 + - + +
445A GLU* 3.2 46.8 + - + +
496A ALA* 3.4 37.2 - - + +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 4.0 11.0 - - - -
143A CYS* 3.6 32.1 - - + -
147A SER* 5.9 0.2 - - - -
434A LEU* 5.0 4.9 - - + -
438A GLY 3.5 14.6 - - - -
439A SER* 2.8 30.8 + - - +
441A PHE* 1.3 76.8 - - - +
443A GLU* 1.3 67.8 + - - +
445A GLU* 3.4 4.5 + - - +
446A LEU* 2.9 50.3 + - + +
481A PHE* 4.2 16.2 - + - -
489A LEU* 4.2 9.2 - - + -
493A GLN 5.2 0.2 - - - -
494A ARG* 3.5 46.7 - - + +
496A ALA* 4.4 10.3 - - + -
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 2.6 18.5 - - - +
435A GLY* 2.4 38.0 - - - +
438A GLY* 3.3 10.2 + - - +
439A SER 2.9 16.7 + - - +
440A GLN 3.4 6.7 - - - +
442A PHE* 1.3 78.7 - - - +
444A ARG* 1.3 53.6 + - - +
446A LEU* 3.0 18.4 + - - +
447A ARG* 2.8 57.8 + - - +
458A LEU* 5.8 0.3 - - - +
538A D3T 3.4 28.3 - - + +
5T A 4.5 4.5 - - + -
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 4.1 23.2 + - - +
176A LEU* 4.3 11.3 - - - +
177A LEU* 2.9 38.3 - - - +
440A GLN* 3.3 36.4 + - - +
441A PHE* 3.6 20.2 - - + +
442A PHE 3.3 0.4 - - - -
443A GLU* 1.3 76.0 - - - +
445A GLU* 1.3 59.1 + - + +
448A ARG* 2.8 32.8 + - - +
4T C 5.2 0.4 - - - +
5T A 2.9 87.2 + - + +
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Residues in contact with GLU 445 (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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140A ALA 3.6 6.8 - - - +
141A TYR* 3.4 10.7 - - - -
142A ALA* 3.1 38.2 + - + +
143A CYS* 3.6 6.9 - - - +
145A ARG* 5.0 1.4 + - - -
177A LEU* 5.9 0.2 - - - +
181A ARG* 3.7 18.6 + - - +
204A TYR* 4.9 0.9 - - - -
441A PHE* 3.2 45.0 + - + +
442A PHE 3.9 3.1 - - - +
444A ARG* 1.3 79.9 - - - +
446A LEU* 1.3 57.4 + - - +
448A ARG* 2.9 32.6 + - - +
449A PHE* 2.8 33.1 + - - +
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Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 3.6 26.4 - - + -
434A LEU* 3.6 35.4 - - + -
442A PHE* 2.9 36.2 + - + +
443A GLU* 3.2 20.0 - - - +
445A GLU* 1.3 78.2 - - - +
447A ARG* 1.3 58.9 + - + +
449A PHE* 3.6 3.5 - - - +
450A SER* 2.9 29.0 + - - -
458A LEU* 3.8 16.3 - - + +
481A PHE* 5.1 6.5 - - + -
484A LEU* 4.8 6.6 - - + +
486A LEU* 4.1 17.3 - - + -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLY* 4.5 8.7 - - - -
443A GLU* 2.8 40.1 + - - +
446A LEU* 1.3 71.4 - - + +
448A ARG* 1.3 64.9 + - - +
450A SER* 3.3 8.5 + - - -
451A ARG* 3.1 22.9 + - - +
458A LEU* 3.6 34.0 + - + +
459A ASN* 3.7 10.5 - - - +
460A SER* 3.5 31.7 - - - +
538A D3T 4.9 4.6 + - - -
5T A 3.1 63.5 + - - +
6T A 3.2 30.6 + - - -
7T T 5.9 0.4 - - - -
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.2 33.8 + - + -
181A ARG* 3.1 35.6 - - - +
204A TYR* 2.7 30.8 + - - -
444A ARG 2.8 19.3 + - - +
445A GLU* 2.9 28.2 + - - +
447A ARG* 1.3 77.4 - - - +
449A PHE* 1.3 55.7 + - - +
451A ARG* 3.1 4.6 + - - +
452A GLN* 2.8 65.8 + - - +
3D C 5.9 2.2 - - - -
4T C 4.6 9.4 - - - -
5T A 3.6 17.4 - - - -
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Residues in contact with PHE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.3 36.3 - + + -
143A CYS* 3.7 6.7 - - - -
144A GLN* 3.3 24.9 - - - -
445A GLU 2.8 20.2 + - - +
446A LEU 3.6 4.3 - - - +
448A ARG* 1.3 73.0 - - - +
450A SER* 1.3 72.1 + - - +
453A GLU* 3.1 42.7 + - + +
454A LYS* 3.6 20.8 + - + +
484A LEU* 3.8 18.8 - - + -
485A GLY 5.2 1.8 - - - -
486A LEU* 3.7 40.2 - - + -
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU 2.9 14.9 + - - -
447A ARG 3.3 10.8 - - - -
448A ARG 3.2 0.2 - - - -
449A PHE* 1.3 80.6 - - - +
451A ARG* 1.3 57.4 + - - +
454A LYS* 2.9 33.1 + - - +
456A LEU* 2.9 22.7 + - - +
458A LEU* 3.7 16.4 + - - -
463A LEU* 3.4 26.3 - - - +
484A LEU* 4.0 10.3 - - - +
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Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG 3.1 9.7 + - - +
448A ARG* 3.7 6.1 - - - +
450A SER* 1.3 74.6 - - - +
452A GLN* 1.3 71.4 + - + +
453A GLU 2.8 9.6 + - - -
455A GLY* 2.9 32.9 + - - +
456A LEU 3.0 13.9 + - - +
457A TRP* 3.2 31.6 - - - +
466A PRO* 5.5 3.6 - - - +
4T C 4.3 17.4 + - - -
5T A 5.5 0.7 - - - -
6T A 3.0 36.0 + - - +
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Residues in contact with GLN 452 (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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141A TYR* 3.4 21.6 + - - +
448A ARG* 2.8 52.4 + - + +
451A ARG* 1.3 84.4 - - + +
453A GLU* 1.3 61.7 + - - +
4D G 6.4 0.4 - - - -
3T G 5.1 0.7 + - - +
4T C 3.7 25.8 - - - +
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.3 41.5 + - + +
449A PHE* 3.1 36.2 + - + +
451A ARG 2.8 1.8 + - - -
452A GLN* 1.3 79.0 - - - +
454A LYS* 1.3 73.5 + - - +
455A GLY 3.9 0.4 - - - -
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Residues in contact with LYS 454 (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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449A PHE* 4.1 26.2 - - + +
450A SER* 2.9 17.1 + - - +
451A ARG 3.1 1.6 + - - -
453A GLU* 1.3 92.8 - - - +
455A GLY* 1.3 55.5 + - - +
456A LEU* 2.6 37.3 + - + +
483A LEU 5.7 1.5 + - - +
484A LEU* 3.6 33.4 + - + +
485A GLY* 5.1 4.6 + - - -
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Residues in contact with GLY 455 (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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451A ARG* 2.9 22.1 + - - -
452A GLN 5.1 0.2 - - - -
453A GLU 3.9 0.4 - - - -
454A LYS* 1.3 73.2 - - - +
456A LEU* 1.3 60.9 + - - +
465A ASP* 4.8 0.2 - - - +
466A PRO* 3.4 26.3 - - - +
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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
------------------------------------------------------------
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