Contacts of the helix formed by residues 331 - 344 (chain A) in PDB entry 4IM0
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 THR 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A ILE* 4.0 2.3 - - - +
329A TYR 4.7 2.2 - - - +
330A ASN* 1.3 78.4 - - - +
332A ALA* 1.3 60.4 + - - +
333A THR* 3.4 9.7 - - - -
334A ILE* 3.2 30.1 + - + +
335A PHE* 3.0 24.1 + - - +
363A PRO 3.3 11.0 - - - -
364A GLY* 4.1 20.2 - - - +
365A ARG 3.5 6.3 - - - -
366A LEU* 4.5 7.6 - - + -
370A PHE* 4.8 1.3 - - - -
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Residues in contact with ALA 332 (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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331A THR* 1.3 72.0 - - - +
333A THR* 1.3 56.0 + - - +
335A PHE* 3.0 2.8 + - - +
336A HIS* 2.8 44.9 + - + +
361A LEU* 3.9 17.0 - - + +
362A GLU 3.3 27.1 - - - +
363A PRO* 3.2 3.7 + - + +
365A ARG 3.0 8.5 + - - +
370A PHE* 3.8 26.5 - - + -
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A THR* 3.4 10.5 - - - +
332A ALA* 1.3 76.9 - - - +
334A ILE* 1.3 66.6 - - + +
336A HIS* 3.3 11.3 + - - +
337A GLU* 3.2 23.2 + - - +
347A SER* 5.3 0.5 + - - -
363A PRO* 3.1 29.2 + - - +
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Residues in contact with ILE 334 (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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308A ARG* 6.3 0.4 - - - +
326A ILE* 4.7 0.2 - - + -
330A ASN* 3.5 40.8 - - + +
331A THR* 3.2 27.4 + - + +
333A THR* 1.3 77.6 - - + +
335A PHE* 1.3 66.9 + - - +
337A GLU* 3.1 17.3 + - - +
338A LEU* 2.9 37.9 + - + +
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Residues in contact with PHE 335 (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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311A ILE* 3.8 33.9 - - + -
313A VAL* 3.6 26.0 - - + -
324A ILE* 4.0 16.2 - - + -
326A ILE* 3.7 14.3 - - + +
331A THR 3.0 13.8 + - - +
332A ALA* 3.2 14.4 - - - +
334A ILE* 1.3 76.7 - - - +
336A HIS* 1.3 67.7 + - - +
338A LEU* 3.2 7.2 + - - +
339A VAL* 3.0 42.6 + - + +
350A GLN* 5.1 0.2 - - - -
352A LEU* 4.0 25.8 - - + -
361A LEU* 4.1 8.5 - - + -
370A PHE* 3.7 21.8 - + + -
379A ILE* 4.7 7.9 - - + -
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Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 2.8 36.6 + - + +
333A THR* 3.6 11.0 - - - +
334A ILE 3.3 0.2 - - - -
335A PHE* 1.3 79.8 - + - +
337A GLU* 1.3 58.0 + - - +
339A VAL 3.2 0.9 + - - +
340A TYR* 2.9 25.5 + - - +
347A SER* 3.8 26.5 - - - +
350A GLN* 2.7 49.1 + - + +
352A LEU* 4.0 27.4 - - + -
361A LEU* 4.5 17.6 + - + +
363A PRO* 6.1 1.6 - - + -
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Residues in contact with GLU 337 (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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333A THR* 3.2 14.3 + - + +
334A ILE* 3.1 21.6 + - + +
336A HIS* 1.3 75.6 - - - +
338A LEU* 1.3 64.7 + - + +
340A TYR* 3.3 12.4 + - + +
341A LYS* 3.0 53.3 + - + +
347A SER* 4.5 5.3 + - - +
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Residues in contact with LEU 338 (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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308A ARG* 5.5 7.2 - - - +
324A ILE* 3.7 26.5 - - + -
325A TYR 3.6 24.9 - - - +
326A ILE* 3.9 18.2 - - + -
330A ASN* 5.4 0.7 - - - +
334A ILE* 2.9 28.3 + - + +
335A PHE 3.2 6.7 + - - +
337A GLU* 1.3 76.9 - - + +
339A VAL* 1.3 62.3 + - - +
341A LYS* 3.4 37.5 + - + +
342A GLN* 3.5 19.6 + - - +
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Residues in contact with VAL 339 (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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313A VAL* 4.4 8.1 - - + -
324A ILE* 4.0 21.8 - - + -
335A PHE* 3.0 47.4 + - + +
336A HIS 3.6 7.0 - - - +
337A GLU 3.2 0.2 - - - -
338A LEU* 1.3 74.7 - - - +
340A TYR* 1.3 61.1 + - - +
342A GLN* 3.1 5.6 + - - +
343A THR* 2.6 49.3 + - + +
350A GLN* 3.7 19.3 - - + +
352A LEU* 6.2 1.1 - - + -
381A VAL* 4.7 16.6 - - + -
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Residues in contact with TYR 340 (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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336A HIS 2.9 13.3 + - - +
337A GLU* 3.6 16.8 - - + +
339A VAL* 1.3 75.7 - - - +
341A LYS* 1.3 68.7 + - + +
343A THR* 3.7 2.0 - - - -
344A LYS* 2.6 77.3 + - + +
345A ILE 3.2 33.9 - - - +
346A ILE* 3.6 23.1 - - + +
347A SER* 4.8 2.7 - - - +
350A GLN* 3.5 2.7 - - - +
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Residues in contact with LYS 341 (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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275A VAL* 6.4 1.3 - - + -
337A GLU* 3.0 45.7 + - - +
338A LEU* 3.5 33.5 - - + +
339A VAL 3.2 0.4 - - - -
340A TYR* 1.3 88.7 - - + +
342A GLN* 1.3 61.8 + - + +
344A LYS* 4.7 12.8 + - - +
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Residues in contact with GLN 342 (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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271A ARG* 4.2 14.5 + - + +
272A GLY* 3.4 27.4 + - - -
275A VAL* 6.2 3.4 - - + -
318A GLN* 5.4 0.5 + - - -
322A HIS* 3.1 49.4 + - + +
323A LYS 3.0 25.2 + - - +
324A ILE* 4.4 11.7 - - + +
325A TYR 5.3 0.8 - - - +
338A LEU* 3.5 10.5 + - - +
339A VAL* 3.1 8.2 + - - +
341A LYS* 1.3 80.0 - - + +
343A THR* 1.3 60.7 + - + +
344A LYS* 5.5 0.9 - - - -
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Residues in contact with THR 343 (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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313A VAL* 5.8 0.2 - - + -
315A SER* 4.2 6.7 - - - +
318A GLN* 2.9 43.3 + - - +
322A HIS* 3.8 25.6 - - + +
339A VAL* 2.6 36.3 + - + +
342A GLN* 1.3 84.3 - - + +
344A LYS* 1.3 70.5 + - - +
345A ILE* 3.2 28.9 + - + +
381A VAL* 4.8 2.2 - - + -
387A LEU* 4.4 1.6 - - - +
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Residues in contact with LYS 344 (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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340A TYR* 2.6 64.0 + - + +
341A LYS* 4.7 10.5 - - - +
342A GLN 5.5 0.7 - - - -
343A THR* 1.3 75.6 - - - +
345A ILE* 1.3 60.2 + - - +
346A ILE* 3.8 2.8 + - - +
387A LEU* 4.8 8.4 - - + +
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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