Contacts of the helix formed by residues 341 - 350 (chain A) in PDB entry 4I6J
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 ASN 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP* 3.4 15.7 + - - +
340A ARG* 1.3 76.5 - - - +
342A PRO* 1.4 69.3 - - - +
343A GLU* 3.2 12.6 + - - +
344A ALA* 3.0 33.6 + - + +
345A LEU* 3.0 23.4 + - - +
388A LEU 5.8 1.6 + - - -
390A VAL* 4.4 11.7 - - + +
90B TYR* 5.3 0.4 + - - -
149B ARG* 3.4 37.6 + - - +
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Residues in contact with PRO 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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340A ARG* 4.5 6.1 - - + +
341A ASN* 1.4 82.7 - - - +
343A GLU* 1.3 59.0 + - + +
345A LEU* 3.7 12.6 - - + +
346A ALA* 2.9 31.0 + - - +
87B ALA 5.5 3.8 - - - +
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Residues in contact with GLU 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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341A ASN* 3.1 9.6 - - - +
342A PRO* 1.3 85.0 - - + +
344A ALA* 1.3 62.2 + - - +
346A ALA* 3.4 5.7 + - - +
347A LYS* 3.2 35.8 + - - +
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Residues in contact with ALA 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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341A ASN* 3.0 32.4 + - + +
343A GLU* 1.3 73.4 - - - +
345A LEU* 1.3 65.3 + - - +
347A LYS* 3.2 10.6 + - - +
348A TRP* 3.1 22.2 + - - +
388A LEU* 3.7 29.1 - - + +
390A VAL* 4.4 6.5 - - + -
488A ILE* 6.2 0.9 - - - -
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Residues in contact with LEU 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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341A ASN 3.0 18.5 + - - +
342A PRO* 3.7 11.0 - - + +
344A ALA* 1.3 76.5 - - - +
346A ALA* 1.3 51.7 + - - +
348A TRP* 3.1 29.8 + - + +
349A ALA* 2.7 37.1 + - + +
383A LEU* 4.3 12.3 - - + -
390A VAL* 4.6 10.8 - - + +
394A SER* 3.9 35.4 - - - +
397A ARG* 4.3 11.0 - - - +
398A VAL* 4.4 12.1 - - + -
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Residues in contact with ALA 346 (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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342A PRO 2.9 18.8 + - - +
343A GLU* 3.5 6.7 - - - +
345A LEU* 1.3 74.0 - - - +
347A LYS* 1.3 65.8 + - + +
349A ALA* 4.2 2.7 - - - -
350A GLU* 2.8 40.9 + - + +
352A LYS* 5.8 1.8 - - - -
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Residues in contact with LYS 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 GLU* 3.2 25.9 + - + +
344A ALA* 3.2 9.8 + - - +
346A ALA* 1.3 78.3 - - + +
348A TRP* 1.3 61.4 + - - +
350A GLU* 4.9 0.2 - - - -
351A GLY 3.4 0.9 + - - -
352A LYS* 2.8 68.4 + - + +
353A THR* 3.6 2.4 + - - +
485A PRO* 6.2 1.6 - - - +
488A ILE* 4.2 33.6 - - + +
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Residues in contact with TRP 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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344A ALA 3.1 10.5 + - - +
345A LEU* 3.1 16.2 + - + +
347A LYS* 1.3 76.0 - - - +
349A ALA* 1.3 79.4 + - - +
350A GLU 3.2 0.7 + - - -
351A GLY* 3.4 3.8 + - - -
353A THR* 3.8 8.4 - - + +
358A ILE* 4.3 8.7 - - + -
362A MET* 3.2 37.4 - - + +
379A VAL* 3.2 47.9 + - + +
382A PHE* 3.8 24.7 - + - -
383A LEU* 3.6 38.7 - - + +
388A LEU* 3.9 11.0 - - + -
395A GLY* 4.2 3.4 - - - -
398A VAL* 3.7 30.5 - - + -
399A PHE* 3.7 21.5 - + - -
415A TRP* 3.9 11.7 - + - -
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Residues in contact with ALA 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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345A LEU* 2.7 21.4 + - + +
346A ALA* 3.1 3.8 + - - +
348A TRP* 1.3 87.0 - - + +
350A GLU* 1.3 73.4 + - - +
351A GLY 3.5 0.4 + - - -
362A MET* 4.1 16.9 - - - +
366A ARG* 2.9 30.5 + - - +
398A VAL* 4.6 13.7 - - + -
402A LEU* 5.1 0.3 - - - +
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Residues in contact with GLU 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 ALA* 2.8 34.0 + - + +
349A ALA* 1.3 88.8 - - - +
351A GLY* 1.3 63.3 + - - +
352A LYS* 3.8 39.1 - - + +
362A MET* 5.0 2.5 - - - -
363A THR* 5.1 3.2 + - - -
366A ARG* 3.3 28.7 + - - +
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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