Contacts of the helix formed by residues 336 - 351 (chain A) in PDB entry 6DWM
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 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A TYR* 2.8 33.8 + - - +
333A LEU 3.6 6.3 - - - +
335A MET* 1.3 92.3 + - - +
337A PRO* 1.3 61.5 - - - +
338A ARG* 3.1 5.2 + - + +
339A VAL* 2.8 39.8 + - + +
340A GLN 3.2 6.8 + - - -
427A PHE* 3.9 31.9 - - + +
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Residues in contact with PRO 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 LEU 3.7 7.4 - - - +
334A VAL 3.8 12.1 - - - +
335A MET 3.5 7.9 - - - +
336A ASN* 1.3 88.4 - - - +
338A ARG* 1.3 62.9 + - - +
340A GLN* 3.0 19.8 + - + +
341A ARG* 3.1 36.1 + - + +
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Residues in contact with ARG 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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336A ASN* 3.0 3.6 + - + +
337A PRO* 1.3 80.1 - - - +
339A VAL* 1.3 83.0 + - + +
341A ARG* 3.6 22.5 + - - +
342A LYS* 3.4 41.1 + - + +
367A TYR* 4.0 1.6 + - - -
427A PHE 4.6 3.4 + - - -
428A LEU* 4.0 17.4 - - - +
429A PRO* 4.5 2.2 - - - +
430A GLU* 2.8 38.0 + - - -
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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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332A TYR 5.6 0.7 - - - +
333A LEU* 4.8 1.6 - - + -
336A ASN* 2.8 30.0 + - + +
338A ARG* 1.3 99.0 - - - +
340A GLN* 1.3 65.6 + - - +
342A LYS 3.7 0.3 + - - -
343A ILE* 3.2 27.3 + - + +
367A TYR* 3.8 22.6 - - + +
371A PHE* 3.7 31.6 - - + -
427A PHE* 4.2 6.1 - - + +
429A PRO* 4.1 17.0 - - + -
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Residues in contact with GLN 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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333A LEU* 3.2 50.4 + - + +
334A VAL* 4.7 0.2 - - - +
336A ASN 3.2 4.0 + - - -
337A PRO* 3.0 14.1 + - - +
339A VAL* 1.3 79.6 - - - +
341A ARG* 1.3 63.8 + - + +
343A ILE* 3.5 4.2 + - - +
344A GLN* 3.2 35.9 + - - +
475A LEU* 3.7 15.0 - - + +
479A GLU* 3.6 10.5 - - - -
480A PHE* 2.8 47.5 + - - +
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Residues in contact with ARG 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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337A PRO* 3.1 36.6 + - + +
338A ARG* 3.6 24.3 + - - +
339A VAL 3.4 0.2 - - - -
340A GLN* 1.3 78.1 - - + +
342A LYS* 1.3 61.1 + - + +
344A GLN* 3.1 18.9 + - - +
345A GLU* 2.8 44.7 + - + +
479A GLU* 5.1 5.6 - - - +
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Residues in contact with LYS 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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338A ARG* 3.4 34.6 + - + +
339A VAL 4.1 0.2 - - - +
340A GLN 3.4 0.2 - - - -
341A ARG* 1.3 77.4 - - + +
343A ILE* 1.3 60.9 + - - +
345A GLU* 3.9 18.8 - - - +
346A GLU* 3.2 21.7 + - - +
367A TYR* 3.8 40.7 - - + +
430A GLU* 3.4 21.6 + - - +
433A LEU* 6.0 0.4 - - - +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.7 19.5 - - + -
339A VAL* 3.2 18.9 + - + +
340A GLN 3.7 6.3 - - - +
341A ARG 3.2 0.6 - - - -
342A LYS* 1.3 75.4 - - - +
344A GLN* 1.3 64.2 + - - +
346A GLU* 3.3 7.8 + - - +
347A LEU* 3.0 30.2 + - + +
367A TYR* 3.5 21.1 - - + +
368A MET* 3.9 35.2 - - + -
371A PHE* 3.7 33.7 - - + -
475A LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 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 GLN* 3.2 32.5 + - - +
341A ARG* 3.1 20.5 + - - +
343A ILE* 1.3 74.9 - - - +
345A GLU* 1.3 65.1 + - + +
347A LEU* 3.1 10.0 + - - +
348A ASP* 2.9 28.6 + - - +
475A LEU* 3.5 26.2 - - + +
478A VAL 3.7 6.6 - - - +
479A GLU* 3.3 41.5 + - - +
511A ARG* 3.4 26.3 - - - +
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Residues in contact with GLU 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 ARG* 2.8 35.9 + - + +
342A LYS* 3.9 19.2 - - - +
344A GLN* 1.3 71.8 - - + +
346A GLU* 1.3 62.9 + - - +
348A ASP* 3.4 7.8 + - - +
349A THR* 3.0 28.6 + - - +
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Residues in contact with GLU 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 LYS 3.2 11.9 + - - +
343A ILE* 3.6 9.7 - - - +
344A GLN 3.2 0.4 - - - -
345A GLU* 1.3 79.4 - - - +
347A LEU* 1.3 57.5 + - - +
349A THR* 3.3 4.1 + - - -
350A VAL* 2.8 40.5 + - + +
365A LEU* 3.4 28.8 - - + +
366A PRO* 3.0 16.3 - - - +
367A TYR* 3.0 27.9 + - + +
368A MET* 3.2 25.8 + - - +
364D HIS* 3.1 30.4 + - + +
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Residues in contact with LEU 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 ILE* 3.0 28.3 + - + +
344A GLN* 3.1 10.3 + - - +
346A GLU* 1.3 76.2 - - - +
348A ASP* 1.3 61.3 + - - +
351A ILE* 2.9 40.8 + - + +
352A GLY 2.9 7.9 + - - +
357A PRO* 4.9 3.4 - - + -
365A LEU* 3.8 31.6 - - + -
368A MET* 5.5 3.1 - - + -
472A ALA* 3.9 24.7 - - + +
475A LEU* 4.2 13.5 - - + -
476A GLN* 3.8 36.1 - - + +
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Residues in contact with ASP 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 GLN 2.9 17.2 + - - +
345A GLU* 3.8 7.2 - - - +
347A LEU* 1.3 78.5 - - - +
349A THR* 1.3 63.8 + - - +
352A GLY* 3.2 24.8 + - - +
353A ARG* 4.0 26.8 + - - +
476A GLN* 5.4 0.5 - - - +
511A ARG* 2.6 41.1 + - - -
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Residues in contact with THR 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 GLU* 3.0 18.4 + - - +
346A GLU* 3.8 5.8 - - - -
348A ASP* 1.3 78.3 - - - +
350A VAL* 1.3 63.8 + - + +
351A ILE 5.2 0.3 - - - -
349D THR* 5.3 5.2 + - - +
350D VAL* 3.6 50.9 + - + +
364D HIS* 4.1 20.4 - - + +
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Residues in contact with VAL 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 GLU* 2.8 31.7 + - + +
349A THR* 1.3 84.2 - - + +
351A ILE* 1.3 66.2 + - + +
355A ARG* 4.7 4.5 + - - -
361A ASP* 5.5 3.1 - - + +
364A HIS* 3.8 37.2 - - + +
365A LEU* 3.8 17.0 - - + -
363D SER 5.8 0.4 - - - +
364D HIS* 4.4 13.9 - - + +
436D ASP 5.0 6.9 - - - +
438D ALA* 5.9 4.0 - - + -
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Residues in contact with ILE 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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347A LEU* 2.9 14.7 + - + +
348A ASP 4.1 0.9 - - - -
349A THR 3.5 0.8 - - - -
350A VAL* 1.3 93.0 - - + +
352A GLY* 1.3 71.3 + - - +
354A SER* 4.7 5.2 + - - -
355A ARG* 3.7 50.3 + - + +
357A PRO* 4.0 22.0 - - + -
361A ASP* 3.3 35.4 - - + +
365A LEU* 4.2 15.3 - - + -
476A GLN* 4.5 2.9 - - + +
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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