Contacts of the helix formed by residues 339 - 348 (chain A) in PDB entry 5K6S
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 HIS 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A HIS* 2.7 48.6 + - + +
298A SER* 3.8 10.5 - - - -
299A PRO* 4.8 14.3 - - + +
337A SER* 3.1 14.9 + - - +
338A PRO* 1.3 84.2 + - + +
340A PHE* 1.3 66.0 + - - +
341A GLN* 4.6 4.0 - - + +
342A VAL* 3.2 22.9 + - + +
343A ALA 3.2 9.4 + - - -
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER 5.3 0.4 - - - -
338A PRO 3.6 4.9 + - - -
339A HIS* 1.3 71.8 - - - +
341A GLN* 1.3 61.3 + - + +
343A ALA* 3.2 7.3 + - + +
344A GLU* 2.7 74.1 + - + +
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Residues in contact with GLN 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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299A PRO* 4.4 21.0 - - + +
302A VAL* 3.8 14.8 - - + +
339A HIS* 3.2 3.1 - - + -
340A PHE* 1.3 83.8 - - + +
342A VAL* 1.3 59.1 + - + +
344A GLU* 3.8 14.0 - - - +
345A ARG* 3.1 28.8 + - - +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A SER 3.8 23.8 - - - +
299A PRO* 4.4 2.5 - - + -
301A GLU* 3.9 30.3 - - + +
302A VAL* 4.1 14.6 - - + -
305A LEU* 3.5 9.5 - - + +
334A CYS* 3.9 19.1 - - + -
337A SER* 3.7 17.3 - - - +
339A HIS* 3.2 25.2 + - + +
341A GLN* 1.3 75.8 - - + +
343A ALA* 1.3 59.0 + - - +
345A ARG* 3.2 1.9 + - - -
346A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 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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334A CYS 3.3 22.1 + - - +
335A VAL* 3.7 16.6 - - - +
337A SER 4.5 6.5 - - - +
339A HIS 3.2 8.3 + - - +
340A PHE* 3.2 12.4 + - + +
342A VAL* 1.3 75.7 - - - +
344A GLU* 1.3 61.0 + - - +
346A ALA* 3.3 1.1 + - - +
347A LEU* 2.9 42.8 + - + +
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Residues in contact with GLU 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 PHE* 2.7 59.2 + - + +
341A GLN* 3.8 12.5 - - - +
343A ALA* 1.3 72.1 - - - +
345A ARG* 1.3 61.5 + - - +
347A LEU* 3.6 9.4 + - - +
348A TYR* 3.3 25.6 + - + +
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Residues in contact with ARG 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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302A VAL* 4.1 18.6 - - + +
305A LEU* 3.7 24.7 - - + -
306A ASN* 3.0 53.3 + - - +
309A GLU* 2.5 34.7 + - - +
341A GLN 3.1 19.9 + - - +
342A VAL* 3.5 4.9 - - - +
343A ALA 3.2 0.2 - - - -
344A GLU* 1.3 75.7 - - - +
346A ALA* 1.3 64.0 + - - +
348A TYR* 3.2 28.2 + - - +
349A TYR* 3.6 8.1 - - - -
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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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305A LEU* 3.9 6.3 - - + +
331A LEU* 3.9 15.1 - - + +
334A CYS* 3.8 24.9 - - + -
335A VAL* 4.2 13.0 - - + +
342A VAL 3.0 15.9 + - - +
343A ALA 3.8 3.4 - - - +
345A ARG* 1.3 76.4 - - - +
347A LEU* 1.3 61.5 + - - +
349A TYR* 3.2 31.8 + - - +
350A TRP* 3.5 8.0 - - - -
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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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335A VAL* 3.9 29.6 - - + -
343A ALA* 2.9 27.6 + - + +
344A GLU* 3.9 7.6 - - - +
345A ARG 3.3 0.2 - - - -
346A ALA* 1.3 72.0 - - - +
348A TYR* 1.3 58.1 + - - +
349A TYR 3.0 9.9 + - - -
350A TRP* 3.2 41.3 + - + +
351A ASN* 4.7 1.7 + - - -
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Residues in contact with TYR 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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309A GLU* 4.3 11.0 - - - +
344A GLU* 3.3 16.1 + - + +
345A ARG* 3.2 32.4 + - - +
346A ALA 3.2 0.6 - - - -
347A LEU* 1.3 74.1 - - - +
349A TYR* 1.3 64.3 + - - +
350A TRP 3.1 1.3 - - - -
351A ASN* 3.1 47.4 + - + +
352A ASN 4.3 0.3 + - - -
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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