Contacts of the helix formed by residues 345 - 356 (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 GLY 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLU 2.8 2.4 + - - -
344B VAL* 1.3 74.3 - - - +
346B LEU* 1.3 65.7 + - - +
347B LEU 3.5 2.2 - - - -
348B PRO* 3.6 15.8 - - - +
349B LYS* 4.2 8.5 + - - +
387B PHE 5.9 1.3 + - - -
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Residues in contact with LEU 346 (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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305B ALA 5.1 0.2 - - - +
306B VAL* 4.9 4.7 - - + +
309B THR* 3.4 29.6 - - + -
310B LEU* 3.9 30.1 - - + +
313B ALA* 4.4 9.4 - - + -
335B ILE* 3.7 30.5 - - + -
336B THR 5.3 0.4 - - - +
343B GLU* 3.1 23.6 + - + +
344B VAL 3.7 0.6 - - - -
345B GLY* 1.3 76.3 - - - +
347B LEU* 1.3 66.0 + - - +
349B LYS* 2.9 16.7 + - - +
350B VAL* 2.9 29.9 + - + +
423B VAL* 4.6 10.1 - - + -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 6.4 1.1 - - + -
345B GLY 5.3 0.2 - - - -
346B LEU* 1.3 76.5 - - - +
348B PRO* 1.3 65.8 - - + +
350B VAL* 2.9 11.9 + - + +
351B MET* 2.9 30.8 + - + +
387B PHE* 3.5 41.7 - - + +
388B GLU 3.7 17.5 - - - +
389B ARG 3.8 12.8 - - - +
390B SER* 3.7 22.0 - - - -
421B LEU* 4.0 21.3 - - + +
423B VAL* 3.7 23.8 - - + +
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Residues in contact with PRO 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLY* 3.6 17.0 - - - +
347B LEU* 1.3 95.5 - - + +
349B LYS* 1.3 54.3 + - - +
351B MET* 3.3 10.2 + - + +
352B SER* 2.9 30.3 + - - -
387B PHE* 3.4 39.3 - - + +
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Residues in contact with LYS 349 (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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309B THR* 3.5 29.8 + - + +
345B GLY 4.2 6.7 + - - +
346B LEU* 2.9 16.0 + - - +
348B PRO* 1.3 80.1 - - - +
350B VAL* 1.3 57.9 + - - +
352B SER* 2.7 19.4 + - - -
353B CYS* 3.3 7.1 + - - +
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Residues in contact with VAL 350 (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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302B ILE* 4.6 2.5 - - + +
305B ALA* 3.4 34.8 - - + +
306B VAL* 4.2 13.2 - - + -
335B ILE* 5.3 5.8 - - + -
346B LEU* 2.9 46.4 - - + +
347B LEU* 3.2 12.1 - - + +
349B LYS* 1.3 76.7 - - - +
351B MET* 1.3 65.3 + - - +
353B CYS* 3.1 5.0 + - - +
354B LEU* 3.0 32.8 + - + +
421B LEU* 4.9 10.5 - - + -
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Residues in contact with MET 351 (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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347B LEU* 2.9 18.3 + - + +
348B PRO* 3.3 11.9 + - + +
350B VAL* 1.3 76.3 - - - +
352B SER* 1.3 57.9 + - - +
354B LEU* 3.5 11.5 + - - +
355B GLN* 2.9 30.8 + - - +
360B VAL* 4.3 17.1 - - + +
363B HIS* 3.7 36.8 - - + +
390B SER* 3.7 28.3 - - - +
392B CYS* 3.9 21.8 - - + -
421B LEU* 4.3 21.1 - - + -
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Residues in contact with SER 352 (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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348B PRO 2.9 14.6 + - - -
349B LYS* 2.7 28.4 + - - -
351B MET* 1.3 75.8 - - - +
353B CYS* 1.3 54.3 + - - +
355B GLN* 2.9 10.8 + - - +
356B SER* 2.7 40.2 + - - -
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Residues in contact with CYS 353 (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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305B ALA* 3.4 26.2 - - + -
308B GLN* 3.5 30.7 - - - +
309B THR* 4.1 7.2 - - - +
349B LYS 3.7 9.4 - - - +
350B VAL 3.1 9.3 + - - +
352B SER* 1.3 82.2 + - - +
354B LEU* 1.3 56.9 + - - +
356B SER* 3.0 27.2 + - - -
357B GLN* 2.8 41.4 + - - +
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Residues in contact with LEU 354 (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* 3.6 28.5 - - + +
302B ILE* 3.9 23.8 - - + -
305B ALA* 3.8 11.4 - - + -
350B VAL* 3.0 30.8 + - + +
351B MET* 3.8 12.8 - - - +
353B CYS* 1.3 75.1 - - - +
355B GLN* 1.3 60.2 - - - +
357B GLN* 3.4 14.8 + - - +
359B LEU* 3.2 46.0 + - + +
360B VAL* 3.9 12.3 - - + +
394B LEU* 4.6 13.2 - - + -
421B LEU* 4.3 9.9 - - + -
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Residues in contact with GLN 355 (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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351B MET* 2.9 14.5 + - - +
352B SER* 2.9 18.7 + - - +
354B LEU* 1.3 76.3 - - - +
356B SER* 1.3 54.6 + - - +
357B GLN 3.0 9.8 + - - -
358B GLY* 3.2 12.6 + - - +
360B VAL* 3.9 31.9 + - - +
363B HIS* 3.2 34.8 + - - -
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Residues in contact with SER 356 (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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352B SER* 2.7 18.0 + - - -
353B CYS* 3.0 13.6 + - - -
355B GLN* 1.3 75.5 - - - +
357B GLN* 1.3 62.3 + - - +
358B GLY 3.6 0.2 - - - -
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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