Contacts of the strand formed by residues 389 - 397 (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 ARG 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B LEU* 3.8 6.4 - - - +
387B PHE* 4.4 4.7 - - - +
388B GLU* 1.3 87.5 + - + +
390B SER* 1.3 62.5 + - - +
391B PHE* 3.9 23.8 - - + -
421B LEU 3.5 5.4 - - - +
422B VAL* 4.4 12.1 - - + +
436B TRP* 3.8 26.8 - - - +
460B SER* 4.2 16.4 + - - -
461B HIS* 5.5 0.8 - - - -
5Q A 4.1 8.5 + - - -
6Q T 3.9 17.6 + - - +
6U A 5.6 1.2 - - - -
7U T 3.4 28.9 + - - -
8U A 3.0 52.9 + - - +
9U C 3.4 23.9 + - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.7 28.7 - - - -
351B MET* 3.7 30.0 - - - +
363B HIS* 5.5 0.2 - - - +
364B GLN* 5.5 7.8 + - - +
387B PHE* 6.0 0.2 - - - -
389B ARG* 1.3 76.1 - - - +
391B PHE* 1.3 66.0 + - - +
392B CYS* 3.5 4.5 + - - +
419B VAL 3.7 1.4 - - - +
421B LEU* 2.9 31.3 + - - +
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 5.1 6.0 - - + -
275B GLN* 6.3 1.1 - - - -
362B TYR* 4.5 7.4 - - - -
363B HIS* 4.5 1.0 - - - -
364B GLN* 4.4 20.5 + - - +
389B ARG* 3.9 35.4 - - + -
390B SER* 1.3 75.4 + - - +
392B CYS* 1.3 59.6 + - - +
418B ARG* 3.2 28.0 - - - +
419B VAL 3.6 4.7 - - - -
420B ASP* 3.4 21.1 - - + -
422B VAL* 5.1 0.7 - - + -
436B TRP* 3.8 14.1 - + - -
5Q A 3.9 25.8 - - - -
6Q T 3.4 34.1 - - + -
8U A 5.3 6.5 - + - -
9U C 5.9 4.9 - - - -
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Residues in contact with CYS 392 (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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244B PHE* 6.0 0.4 - - - -
351B MET* 3.9 27.1 - - + -
362B TYR* 3.3 22.0 - - - +
363B HIS* 4.4 1.3 - - - -
390B SER* 4.4 5.4 - - - +
391B PHE* 1.3 76.0 - - - +
393B ILE* 1.3 61.0 + - - +
394B LEU* 3.7 32.8 - - - -
418B ARG* 3.5 7.7 + - - +
419B VAL* 2.7 53.7 + - - -
421B LEU* 5.2 3.6 - - - -
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Residues in contact with ILE 393 (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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244B PHE* 4.0 24.5 - - + -
278B ALA* 4.2 24.2 - - + +
282B TYR* 4.6 6.1 - - + -
286B LEU* 3.8 30.1 - - + -
361B LEU* 2.8 36.4 + - + -
362B TYR* 3.3 24.1 + - + +
392B CYS* 1.3 77.5 - - - +
394B LEU* 1.3 64.0 + - - +
416B ALA* 4.0 25.8 - - + -
417B VAL 3.4 9.2 - - - +
418B ARG* 4.8 7.0 - - + -
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Residues in contact with LEU 394 (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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298B LEU* 5.1 13.5 - - + -
301B LEU* 6.5 1.1 - - + -
302B ILE* 4.4 20.6 - - + -
354B LEU* 4.6 14.4 - - + -
359B LEU* 3.2 22.4 - - + +
360B VAL* 3.6 27.6 - - + -
361B LEU* 4.2 4.3 - - - -
392B CYS* 3.7 25.4 - - - -
393B ILE* 1.3 74.4 - - - +
395B GLY* 1.3 65.0 + - - +
396B LEU 3.6 0.6 + - - -
415B LYS 3.6 0.2 - - - +
416B ALA* 3.5 2.6 - - - -
417B VAL* 2.8 36.8 + - + +
419B VAL* 3.9 24.0 - - + -
421B LEU* 5.9 0.2 - - + -
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Residues in contact with GLY 395 (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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298B LEU* 5.4 1.2 - - - +
301B LEU* 5.3 1.0 - - - +
359B LEU* 2.9 30.5 + - - +
361B LEU* 4.1 18.1 - - - +
394B LEU* 1.3 73.7 - - - +
396B LEU* 1.3 60.7 + - - -
397B PRO* 2.9 15.6 - - - +
414B TRP* 4.4 14.1 - - - -
415B LYS 3.9 3.8 - - - -
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Residues in contact with LEU 396 (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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294B ASP* 2.9 45.1 - - + +
297B ALA* 4.0 23.6 - - + -
298B LEU* 3.7 25.1 - - + +
301B LEU* 5.0 2.5 - - + -
394B LEU 3.6 1.4 + - - -
395B GLY* 1.3 68.8 - - - -
397B PRO* 1.3 85.2 - - + +
398B GLN* 3.1 23.9 + - + +
414B TRP* 3.3 2.0 - - - -
415B LYS* 3.0 34.3 + - - +
417B VAL* 3.9 15.9 - - + -
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Residues in contact with PRO 397 (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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301B LEU* 4.4 12.1 - - + -
359B LEU* 3.8 20.0 - - + -
395B GLY 2.9 17.2 - - - +
396B LEU* 1.3 92.7 - - + +
398B GLN* 1.3 63.7 + - - +
399B PRO* 4.8 0.2 - - - +
413B THR 4.1 5.4 - - - +
414B TRP* 4.3 4.3 - - + -
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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
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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