Contacts of the helix formed by residues 428 - 438 (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 GLN 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A THR* 3.5 8.5 - - - +
425A PRO* 2.9 39.7 + - + +
427A SER* 1.3 84.1 - - - +
429A PHE* 1.3 60.7 + - - +
430A PRO* 3.3 4.9 - - - -
431A PHE* 3.2 10.4 + - + +
432A ALA* 3.1 19.2 + - - +
460A SER 4.3 0.9 - - - +
461A HIS* 3.1 61.9 + - + +
464A PHE* 6.1 0.4 - - - -
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Residues in contact with PHE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A THR* 5.4 1.3 - - - -
316A THR* 3.8 22.2 - - + -
334A LEU* 3.4 32.1 - - + -
336A THR* 3.5 30.3 - - + -
424A THR* 3.8 13.2 - - + -
425A PRO 3.1 5.1 + - - +
426A SER* 3.8 21.1 - - - +
428A GLN* 1.3 75.3 - - - +
430A PRO* 1.3 74.2 - - + +
432A ALA* 3.1 0.6 + - - +
433A LEU* 2.8 59.9 + - + +
475A THR 5.5 2.2 - - - -
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Residues in contact with PRO 430 (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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426A SER 3.9 9.0 - - - +
427A SER 4.2 0.4 - - - +
428A GLN* 3.4 6.5 - - - -
429A PHE* 1.3 102.4 - - + +
431A PHE* 1.3 58.9 + - + +
433A LEU* 4.1 4.9 - - + +
434A LEU* 3.2 25.1 + - - +
474A ALA* 3.6 23.1 - - + +
475A THR* 3.4 30.7 - - - +
476A SER* 3.6 24.5 - - - +
477A GLU* 4.3 7.6 - - + +
480A VAL* 4.2 7.1 - - + +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER 4.9 4.7 - - - -
428A GLN* 3.2 13.1 + - - +
429A PHE 3.1 0.8 - - - -
430A PRO* 1.3 78.8 - - + +
432A ALA* 1.3 66.6 + - - +
434A LEU* 3.7 5.4 - - + +
435A GLY* 3.0 20.1 + - - -
458A LEU* 3.8 15.8 - - + +
459A ASN 4.1 2.9 - - - +
460A SER* 3.3 21.0 - - - +
461A HIS 3.5 20.0 - - - -
462A GLY* 3.3 17.5 - - - +
463A LEU* 3.4 33.7 - - + -
472A PHE* 5.1 5.8 - - + -
473A HIS* 4.6 8.3 - - - -
474A ALA* 3.8 25.8 - - + -
480A VAL* 3.6 28.3 - - + -
483A LEU* 4.8 4.9 - - + -
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Residues in contact with ALA 432 (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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334A LEU* 3.6 28.5 - - + -
422A VAL* 5.3 2.0 - - + -
424A THR* 3.8 16.2 - - + +
428A GLN 3.1 11.7 + - - +
429A PHE 3.1 7.8 + - - +
431A PHE* 1.3 77.7 - - - +
433A LEU* 1.3 56.9 + - - +
435A GLY 3.3 0.7 + - - -
436A TRP* 2.9 37.7 + - + +
460A SER* 3.2 19.0 + - - +
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Residues in contact with LEU 433 (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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316A THR* 3.8 18.6 - - + -
318A THR* 3.5 28.7 - - + -
322A ARG* 3.5 36.6 - - - +
334A LEU* 3.3 14.5 - - + +
429A PHE* 2.8 37.1 + - + +
430A PRO* 4.2 4.5 - - + +
432A ALA* 1.3 78.3 - - - +
434A LEU* 1.3 60.9 + - - +
436A TRP 3.8 0.2 - - - -
437A THR* 2.7 32.3 + - - +
477A GLU* 3.8 15.0 - - + +
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Residues in contact with LEU 434 (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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430A PRO 3.2 17.8 + - - +
431A PHE* 3.7 7.2 - - - +
432A ALA 3.3 0.2 - - - -
433A LEU* 1.3 81.9 - - - +
435A GLY* 1.3 53.0 + - - +
437A THR* 3.7 5.9 + - - -
438A GLY 3.9 3.8 + - - +
442A PHE* 5.0 5.2 - - + -
443A GLU* 2.6 21.7 - - - +
446A LEU* 3.6 30.0 - - + +
458A LEU* 4.2 14.1 - - + -
477A GLU* 3.5 23.3 + - + +
480A VAL* 3.5 29.8 - - + -
481A PHE* 3.8 29.4 - - + -
494A ARG* 4.1 6.7 + - - +
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Residues in contact with GLY 435 (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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431A PHE 3.0 15.1 + - - -
432A ALA* 3.8 2.2 - - - -
434A LEU* 1.3 74.1 - - - +
436A TRP* 1.3 60.7 + - - +
443A GLU* 2.4 38.4 - - - +
447A ARG* 4.5 13.2 - - - -
459A ASN 6.1 0.2 - - - -
460A SER* 5.3 3.1 - - - -
538A D3T 3.2 18.2 - - - +
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Residues in contact with TRP 436 (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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318A THR* 3.5 18.5 + - + +
319A GLY* 2.8 25.5 + - - -
332A ASP* 3.5 34.3 - - + -
333A PHE 6.0 1.1 - - - -
334A LEU* 5.1 3.6 - - + -
389A ARG* 3.8 27.8 - - - +
391A PHE* 3.7 17.0 - + - -
420A ASP* 4.0 10.3 - - + -
422A VAL* 3.5 39.7 - - + +
432A ALA* 2.9 30.4 + - + +
433A LEU 3.8 0.4 - - - -
435A GLY* 1.3 77.0 - - - +
437A THR* 1.3 59.6 + - - +
438A GLY 3.4 0.2 - - - -
460A SER* 4.0 20.1 + - - -
538A D3T 3.3 24.8 - - - +
6P T 3.5 30.7 - - + -
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Residues in contact with THR 437 (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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318A THR* 4.3 1.4 - - - +
319A GLY 3.7 9.0 - - - +
322A ARG* 3.0 38.5 + - + +
323A ARG* 3.0 40.4 + - + +
433A LEU* 2.7 24.7 + - - +
434A LEU 4.1 1.8 - - - -
435A GLY 3.3 0.6 - - - -
436A TRP* 1.3 79.0 - - - +
438A GLY* 1.3 62.8 + - - +
491A PRO* 4.2 7.0 - - + -
494A ARG* 3.6 24.2 - - - +
538A D3T 4.3 1.3 - - - -
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Residues in contact with GLY 438 (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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323A ARG* 3.7 1.9 - - - -
434A LEU 3.9 0.7 + - - +
436A TRP 3.4 2.2 - - - -
437A THR* 1.3 84.2 - - - +
439A SER* 1.3 70.9 + - - -
442A PHE* 3.5 11.6 - - - -
443A GLU* 3.3 12.6 + - - +
494A ARG* 3.4 26.0 - - - +
538A D3T 3.4 14.4 - - - -
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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