Contacts of the helix formed by residues 344 - 356 (chain A) in PDB entry 5IKP
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 LEU 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A LEU* 4.3 12.1 - - + +
296A GLU* 5.0 5.6 - - + +
297A TYR* 4.1 21.3 - - + +
300A VAL* 3.5 21.1 - - + -
341A HIS 4.6 2.1 + - - +
342A PRO 2.8 2.2 + - - -
343A ALA* 1.3 75.5 - - - +
345A SER* 1.3 64.2 + - - +
346A ILE 3.0 3.8 + - - -
347A PRO* 3.2 22.8 - - + +
348A GLU* 3.0 23.6 + - - +
392A PHE* 3.7 35.9 - - + -
396A LEU* 3.8 21.5 - - + -
399A HIS* 4.1 16.6 - - + -
403A ILE* 4.5 1.8 - - + -
441A MET* 4.2 8.3 - - + +
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Residues in contact with SER 345 (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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85A LEU* 3.4 13.1 - - - +
300A VAL* 3.3 23.3 - - - +
304A LEU* 3.3 18.9 - - - +
335A ILE* 4.7 5.6 - - - -
337A LEU* 3.3 21.5 - - - +
342A PRO 2.8 21.3 + - - -
344A LEU* 1.3 75.9 - - - +
346A ILE* 1.3 53.5 + - - +
349A LEU* 2.8 36.7 + - - +
372A CYS* 5.0 5.6 - - - -
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.7 23.8 - - + -
343A ALA 3.7 10.1 + - - +
344A LEU 3.0 1.4 + - - -
345A SER* 1.3 78.9 - - - +
347A PRO* 1.4 73.1 - - + +
349A LEU* 3.7 2.3 - - - +
350A MET* 3.2 21.2 + - - +
365A TRP* 4.0 18.2 - - + -
368A THR* 4.0 9.4 - - + +
372A CYS* 4.1 20.2 - - - -
406A ILE* 4.6 1.8 - - + -
444A LEU* 3.4 32.5 - - + +
445A CYS* 3.8 14.8 - - + +
448A GLY* 3.9 27.1 - - - +
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Residues in contact with PRO 347 (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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343A ALA 3.6 9.4 - - - +
344A LEU* 3.2 28.5 - - + +
346A ILE* 1.4 91.9 - - + +
348A GLU* 1.3 53.8 + - - +
350A MET* 3.4 4.5 - - + +
351A ARG* 2.9 28.4 + - - +
399A HIS* 4.1 12.6 - - + +
402A ILE* 3.7 26.2 - - + +
403A ILE* 3.8 35.0 - - + -
406A ILE* 4.5 3.1 - - + -
444A LEU* 3.9 8.3 - - + -
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Residues in contact with GLU 348 (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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297A TYR* 2.8 18.6 + - - -
300A VAL* 3.7 22.7 - - + -
301A ALA* 3.6 17.2 - - - +
304A LEU* 3.8 6.5 - - + -
305A GLN* 4.3 3.3 + - - -
344A LEU 3.0 19.1 + - - +
345A SER 4.0 1.3 - - - +
347A PRO* 1.3 73.1 - - - +
349A LEU* 1.3 60.3 + - - +
351A ARG* 2.8 28.6 + - - +
352A ILE* 2.9 56.1 + - + +
399A HIS* 2.8 36.7 + - + +
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Residues in contact with LEU 349 (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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304A LEU* 3.6 17.2 - - + +
307A ILE* 6.2 0.4 - - + -
308A ILE* 3.9 27.1 - - + -
329A PHE* 4.2 19.1 - - + -
335A ILE* 5.2 4.7 - - + -
345A SER 2.8 23.4 + - - +
346A ILE* 3.7 4.0 - - - +
348A GLU* 1.3 70.0 - - - +
350A MET* 1.3 66.6 + - - +
352A ILE* 3.4 3.2 + - - +
353A LEU* 2.9 41.0 + - + +
367A ILE* 4.8 0.4 - - + -
368A THR* 3.5 23.6 - - + +
371A THR* 3.5 30.5 - - + -
372A CYS* 5.3 4.0 - - - -
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Residues in contact with MET 350 (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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346A ILE 3.2 16.2 + - - +
347A PRO* 3.4 9.6 - - + +
349A LEU* 1.3 77.3 - - - +
351A ARG* 1.3 55.1 + - - +
353A LEU* 3.7 2.8 - - - +
354A VAL* 2.8 46.4 + - + +
361A TRP* 3.6 59.9 - - + +
364A ALA* 3.7 4.7 - - + +
365A TRP* 3.5 34.5 - - + +
368A THR* 3.2 22.0 - - - +
402A ILE* 3.7 19.7 - - + -
406A ILE* 4.6 2.0 - - + -
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Residues in contact with ARG 351 (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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201A HIS* 6.1 5.4 - - - -
215A TRP* 4.1 21.4 - - - +
297A TYR* 4.1 5.3 + - - -
305A GLN* 4.8 10.3 - - - +
347A PRO 2.9 15.7 + - - +
348A GLU* 2.8 46.0 + - - +
350A MET* 1.3 72.8 - - - +
352A ILE* 1.4 73.1 + - - +
354A VAL* 5.1 0.9 - - - -
355A ASP* 2.7 59.5 + - - +
356A VAL* 4.5 16.4 - - - +
398A ARG* 4.0 15.5 - - + +
399A HIS* 3.7 18.8 - - - +
402A ILE* 3.7 9.7 - - + +
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Residues in contact with ILE 352 (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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304A LEU* 3.8 21.8 - - + -
305A GLN* 4.4 16.2 - - + -
308A ILE* 3.5 30.5 - - + -
348A GLU* 2.9 53.2 + - + +
349A LEU* 3.9 2.9 - - - +
351A ARG* 1.4 81.2 - - - +
353A LEU* 1.3 57.5 + - - +
356A VAL* 3.2 25.7 + - + +
357A GLU* 2.9 39.4 + - + +
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Residues in contact with LEU 353 (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 ILE* 5.6 3.4 - - + -
326A PHE* 3.7 46.0 - - + -
329A PHE* 5.8 2.0 - - + -
349A LEU* 2.9 47.9 + - + +
350A MET 3.8 2.0 - - - +
352A ILE* 1.3 75.8 - - + +
354A VAL* 1.3 57.6 + - - +
357A GLU* 3.3 6.8 - - + +
358A LYS 3.2 10.7 + - - -
359A VAL* 2.9 36.2 + - + +
364A ALA* 3.8 37.5 - - + +
367A ILE* 4.3 11.2 - - + -
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Residues in contact with VAL 354 (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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213A VAL* 5.6 2.2 - - + -
350A MET* 2.8 26.2 + - + +
351A ARG* 4.2 0.4 - - - +
353A LEU* 1.3 75.7 - - - +
355A ASP* 1.3 73.5 + - - +
358A LYS* 3.5 18.2 + - - +
359A VAL 3.6 15.2 - - - +
361A TRP* 3.9 50.3 - - + +
364A ALA* 4.1 11.0 - - + -
398A ARG* 4.7 7.2 - - - +
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Residues in contact with ASP 355 (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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212A GLY* 5.9 0.7 - - - -
213A VAL* 3.4 33.9 - - - +
214A LYS* 3.5 10.4 + - - -
351A ARG* 2.7 41.2 + - + +
354A VAL* 1.3 76.9 - - - +
356A VAL* 1.3 62.7 + - + +
358A LYS* 3.2 22.6 + - - +
398A ARG* 2.8 45.9 + - - +
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Residues in contact with VAL 356 (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 ARG* 4.5 20.9 - - - +
352A ILE* 3.2 30.5 + - + +
355A ASP* 1.3 79.2 - - + +
357A GLU* 1.3 74.4 + - - +
358A LYS* 3.2 13.9 + - - +
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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