Contacts of the strand formed by residues 389 - 397 (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 ARG 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A LEU* 3.3 7.0 - - - +
364A GLN 3.8 0.3 - - - +
365A TYR* 3.4 4.3 - - - +
366A HIS* 2.7 71.0 + - + +
387A PHE* 4.1 0.2 - - - -
388A GLU* 1.3 100.2 - - + +
390A SER* 1.3 60.6 + - - +
391A PHE* 3.4 25.0 - - + -
421A LEU 3.3 2.7 - - - +
422A VAL* 3.9 26.9 - - + -
436A TRP* 3.8 19.7 - - - +
460A SER* 5.8 4.2 + - - -
5P A 5.8 2.0 - - - -
6P T 5.0 9.5 + - - -
7T T 4.7 8.5 + - - -
8T A 3.2 26.5 + - - -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.5 20.2 - - - -
351A MET* 3.5 13.3 - - - -
364A GLN 3.6 4.4 + - - -
365A TYR* 3.6 16.9 - - - -
389A ARG* 1.3 75.5 - - - +
391A PHE* 1.3 62.7 + - - +
392A CYS* 3.3 21.2 - - - +
419A VAL 3.6 2.3 - - - +
420A ASP* 3.2 4.7 - - - -
421A LEU* 2.8 45.1 + - - +
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Residues in contact with PHE 391 (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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244A PHE* 6.0 3.1 - - + -
362A TYR* 3.8 7.2 - - + -
363A HIS* 3.4 1.7 - - - -
364A GLN* 2.9 40.0 + - + +
366A HIS* 3.7 26.2 - + - +
389A ARG* 3.4 51.6 - - + -
390A SER* 1.3 76.9 - - - +
392A CYS* 1.3 59.9 + - - +
418A ARG* 4.5 6.7 - - - +
420A ASP* 3.4 20.6 - - + +
421A LEU 5.5 0.7 - - - -
422A VAL* 5.5 0.2 - - + -
436A TRP* 3.7 18.4 - + - -
5P A 5.2 10.5 - - - -
6P T 3.1 41.3 - - + -
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Residues in contact with CYS 392 (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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351A MET* 3.9 16.6 - - + -
362A TYR* 2.8 27.1 - - - +
363A HIS* 3.5 9.6 - - + +
390A SER* 3.3 24.2 - - - -
391A PHE* 1.3 74.9 - - - +
393A ILE* 1.3 63.5 + - - +
394A LEU* 4.3 15.3 - - + -
418A ARG* 3.0 11.6 + - - +
419A VAL* 2.8 40.6 + - - -
421A LEU* 5.3 4.3 - - - -
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Residues in contact with ILE 393 (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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244A PHE* 4.2 13.9 - - + -
278A ALA* 4.2 5.4 - - + -
282A TYR* 4.2 14.6 - - + -
286A LEU* 4.2 23.6 - - + -
361A LEU* 2.9 36.0 + - + +
362A TYR* 3.1 37.0 + - + +
392A CYS* 1.3 81.3 - - - +
394A LEU* 1.3 65.4 + - - +
416A ALA* 4.0 26.7 - - + -
417A VAL 3.2 13.0 - - - +
418A ARG* 3.8 15.0 - - + -
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Residues in contact with LEU 394 (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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298A LEU* 4.3 19.5 - - + -
301A LEU* 6.2 1.8 - - + -
302A ILE* 4.7 8.1 - - + -
354A LEU* 4.4 26.5 - - + -
359A LEU* 3.4 11.2 - - + +
360A VAL* 3.9 28.9 - - + -
361A LEU* 4.2 3.4 - - - -
392A CYS* 4.3 15.9 - - - -
393A ILE* 1.3 82.7 - - - +
395A GLY* 1.3 61.7 + - - +
396A LEU 3.2 5.1 + - - -
415A LYS 3.5 0.3 - - - +
416A ALA* 3.5 1.0 - - - -
417A VAL* 2.8 34.9 + - + +
419A VAL* 3.9 33.0 - - + -
421A LEU* 6.1 0.2 - - + -
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Residues in contact with GLY 395 (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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359A LEU* 2.8 47.3 + - - +
361A LEU* 3.8 18.4 - - - +
394A LEU* 1.3 71.8 - - - +
396A LEU* 1.3 59.2 + - - -
397A PRO* 3.0 4.3 - - - +
414A TRP* 4.3 12.4 - - - +
415A LYS 3.7 5.8 - - - -
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Residues in contact with LEU 396 (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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294A ASP* 3.6 46.2 - - + +
297A ALA* 4.0 21.3 - - + -
298A LEU* 3.8 28.5 - - + -
301A LEU* 4.4 8.5 - - + -
394A LEU* 3.2 4.7 + - - +
395A GLY* 1.3 69.7 - - - -
397A PRO* 1.3 86.1 - - + +
398A GLN* 3.9 9.5 - - + +
414A TRP* 3.7 0.8 - - - -
415A LYS* 2.8 37.9 + - + +
417A VAL* 4.3 15.9 - - + -
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Residues in contact with PRO 397 (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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301A LEU* 4.8 10.1 - - + -
359A LEU* 3.9 14.6 - - + -
395A GLY 3.0 12.7 - - - +
396A LEU* 1.3 103.5 - - + +
398A GLN* 1.3 65.0 + - - +
413A THR 3.7 9.4 - - - +
414A TRP* 4.1 6.7 - - + -
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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