Contacts of the helix formed by residues 439 - 453 (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 SER 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A D3T 4.9 0.7 - - - -
323B ARG* 3.6 24.4 - - - +
438B GLY* 1.3 74.8 + - - -
440B GLN* 1.3 66.3 + - - +
441B PHE 3.5 1.5 + - - -
442B PHE* 2.7 26.3 + - - +
443B GLU* 2.9 13.0 + - - +
494B ARG 3.0 17.0 + - - -
495B ASN* 4.5 0.9 - - - -
496B ALA 2.8 34.1 + - - -
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Residues in contact with GLN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A D3T 3.5 68.9 + - + +
176B LEU* 6.2 0.2 - - - +
438B GLY* 4.0 0.8 - - - -
439B SER* 1.3 75.7 - - - +
441B PHE* 1.3 65.3 + - - +
443B GLU* 3.1 13.0 + - - +
444B ARG* 3.3 26.4 + - - +
5U A 4.4 10.4 + - - +
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Residues in contact with PHE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 3.9 4.9 - - + -
145B ARG* 4.8 2.2 - - - -
177B LEU* 4.0 17.5 - - + -
180B SER* 4.3 15.5 - - - -
181B ARG* 3.4 40.4 - - + -
184B SER* 3.5 24.2 - - - -
439B SER* 3.2 1.4 + - - -
440B GLN* 1.3 78.2 - - + +
442B PHE* 1.3 64.5 + - - +
444B ARG* 3.5 15.2 + - + +
445B GLU* 3.2 56.1 + - + +
496B ALA* 3.5 34.1 - - + +
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Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 3.9 13.7 - - - -
143B CYS* 3.8 25.5 - - + +
434B LEU* 4.4 3.6 - - + -
438B GLY 3.5 15.0 - - - -
439B SER* 2.7 37.8 + - - +
441B PHE* 1.3 73.7 - - - +
443B GLU* 1.3 61.6 + - - -
445B GLU* 3.3 5.0 + - - +
446B LEU* 2.8 51.0 + - + +
481B PHE* 3.9 22.9 - + - -
489B LEU* 4.3 7.6 - - + -
493B GLN 4.8 1.1 - - - -
494B ARG* 3.4 46.2 - - + +
496B ALA* 4.5 11.9 - - + +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A D3T 3.5 28.0 - - + +
434B LEU 2.7 21.3 - - - +
435B GLY* 3.2 32.5 + - - +
438B GLY* 3.2 18.7 + - - +
439B SER 2.9 10.9 + - - +
440B GLN 3.1 6.0 + - - +
442B PHE* 1.3 82.7 - - - +
444B ARG* 1.3 58.1 + - - +
446B LEU* 3.2 13.1 + - - +
447B ARG* 2.8 49.7 + - - +
5U A 4.4 7.4 - - + -
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Residues in contact with ARG 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU* 4.9 12.3 + - - +
176B LEU* 4.4 16.6 - - - +
177B LEU* 3.4 32.8 - - - +
440B GLN* 3.3 28.0 + - - +
441B PHE* 3.8 20.7 - - + +
442B PHE 3.3 0.2 - - - -
443B GLU* 1.3 76.0 - - - +
445B GLU* 1.3 60.9 + - + +
448B ARG* 2.9 30.8 + - - +
4U C 5.1 0.2 - - - +
5U A 2.7 100.5 + - + +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 3.6 5.4 - - - +
141B TYR* 3.5 22.8 - - + -
142B ALA* 3.5 20.4 + - + +
143B CYS* 3.7 4.4 - - - +
145B ARG* 5.8 0.3 + - - -
177B LEU* 5.1 0.9 - - - +
181B ARG* 3.3 27.2 + - - +
204B TYR* 5.2 0.2 + - - -
441B PHE* 3.2 51.9 + - + +
442B PHE 3.8 2.9 - - - +
444B ARG* 1.3 75.5 - - - +
446B LEU* 1.3 61.5 + - - +
448B ARG* 3.3 26.2 + - - -
449B PHE* 2.9 32.1 + - - +
5U A 5.4 0.9 + - - -
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Residues in contact with LEU 446 (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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143B CYS* 3.8 26.4 - - + +
434B LEU* 3.5 37.0 - - + -
442B PHE* 2.8 36.7 + - + +
443B GLU* 3.5 17.0 - - - +
445B GLU* 1.3 78.1 - - - +
447B ARG* 1.3 56.8 + - + +
449B PHE* 3.7 2.9 - - - +
450B SER* 3.0 28.3 + - - -
458B LEU* 3.7 18.2 - - + -
480B VAL* 6.3 0.9 - - + -
481B PHE* 5.0 6.1 - - + -
484B LEU* 5.9 2.7 - - + -
486B LEU* 3.8 19.5 - - + -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A D3T 4.9 4.0 + - - -
435B GLY* 4.4 7.1 + - - -
443B GLU* 2.8 39.9 + - - +
446B LEU* 1.3 76.8 - - + +
448B ARG* 1.3 64.5 + - - +
450B SER* 3.4 9.1 + - - -
451B ARG* 3.0 23.9 + - - +
456B LEU 4.7 0.2 - - - +
458B LEU* 3.6 32.8 + - + +
459B ASN* 3.8 11.3 - - - +
460B SER* 3.4 30.7 + - - +
5U A 3.3 47.6 + - - +
6U A 3.0 44.1 + - - +
7U T 5.2 1.0 + - - -
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 5.5 0.2 - - - +
141B TYR* 2.9 46.6 + - + -
181B ARG* 3.4 28.3 - - - +
204B TYR* 2.8 27.7 + - - -
444B ARG 2.9 19.2 + - - +
445B GLU* 3.3 26.3 + - - +
447B ARG* 1.3 74.4 - - - +
449B PHE* 1.3 60.9 + - - +
451B ARG* 4.8 2.7 - - - +
452B GLN* 2.9 59.4 + - + +
4U C 4.7 6.6 - - - -
5U A 3.7 23.1 - - - -
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Residues in contact with PHE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.3 31.4 - + + -
143B CYS* 3.6 10.1 - - - -
144B GLN* 3.6 25.1 - - - -
445B GLU 2.9 17.8 + - - +
446B LEU 3.7 2.7 - - - +
448B ARG* 1.3 75.1 - - - +
450B SER* 1.3 70.9 + - - +
453B GLU* 2.9 58.9 + - + +
454B LYS* 3.5 17.5 + - + -
484B LEU* 3.8 18.6 - - + -
485B GLY 4.7 2.7 - - - -
486B LEU* 3.2 36.1 - - + -
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Residues in contact with SER 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU 3.0 20.2 + - - -
447B ARG* 3.4 10.8 - - - -
449B PHE* 1.3 82.0 - - - +
451B ARG* 1.3 57.2 + - - +
454B LYS* 3.4 16.9 + - - +
456B LEU* 2.9 26.8 + - - +
458B LEU* 3.4 27.0 - - - +
463B LEU* 3.5 16.8 - - - +
484B LEU* 5.4 10.2 - - - +
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Residues in contact with ARG 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG 3.0 14.5 + - - +
448B ARG* 4.0 2.9 - - - +
449B PHE 2.9 2.0 + - - -
450B SER* 1.3 75.0 - - - +
452B GLN* 1.3 75.1 + - + +
453B GLU 3.1 1.8 - - - -
455B GLY* 2.8 31.4 + - - -
456B LEU 3.2 15.9 - - - +
457B TRP* 3.0 55.1 - - + +
4U C 4.3 16.2 + - - -
5U A 5.1 1.8 - - - -
6U A 3.2 33.8 + - - +
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Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.6 14.4 + - - +
448B ARG* 2.9 52.2 + - + +
451B ARG* 1.3 89.6 - - + +
453B GLU* 1.3 66.0 + - - +
3U G 5.4 0.6 + - - -
4U C 4.4 23.4 + - - +
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 2.8 30.1 + - + +
449B PHE* 2.9 55.1 + - + +
452B GLN* 1.3 86.1 - - - +
454B LYS* 1.3 67.0 + - + +
455B GLY 3.7 1.1 - - - -
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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