Contacts of the helix formed by residues 344 - 354 (chain A) in PDB entry 5C16
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 GLN 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A ARG* 1.3 77.7 - - - +
345A ASN* 1.3 66.3 + - - +
346A SER* 4.1 16.7 + - - +
347A VAL* 3.1 25.1 + - + +
348A ALA* 3.0 19.8 + - - +
371A PHE* 4.3 0.4 - - - -
373A GLU* 3.4 42.6 + - + +
374A ILE 3.9 3.5 + - - +
375A HIS* 3.6 44.2 + - - +
376A ASN 4.8 0.9 + - - -
444A ARG* 5.7 0.2 + - - -
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Residues in contact with ASN 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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343A ARG 3.8 1.0 + - - -
344A GLN* 1.3 70.3 - - - +
346A SER* 1.3 62.5 - - - +
348A ALA* 3.3 3.5 + - - +
349A ASP* 3.1 34.7 + - - +
358A TYR* 4.3 3.5 + - - -
371A PHE* 3.5 41.5 - - + -
373A GLU* 2.9 18.1 + - - +
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Residues in contact with SER 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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344A GLN* 4.1 16.0 + - - +
345A ASN* 1.3 79.9 - - - +
347A VAL* 1.3 69.4 + - - +
349A ASP* 3.2 9.7 + - - +
350A THR* 3.1 26.0 + - - -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 4.3 17.9 - - + -
344A GLN* 3.1 34.5 + - + +
346A SER* 1.3 85.1 + - - +
348A ALA* 1.3 64.8 + - - +
349A ASP 3.1 0.2 - - - -
350A THR* 3.5 7.6 + - - -
351A ASN* 2.9 43.8 + - - +
376A ASN* 5.6 13.7 - - + +
439A SER* 5.3 0.2 - - - +
444A ARG* 4.9 10.1 - - - +
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Residues in contact with ALA 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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343A ARG* 3.8 27.1 - - - +
344A GLN 3.0 8.7 + - - +
345A ASN 3.7 4.9 - - - +
346A SER 3.3 0.2 - - - -
347A VAL* 1.3 79.3 - - - +
349A ASP* 1.3 56.3 + - - +
351A ASN* 3.5 2.8 + - - +
352A LYS* 3.0 24.6 + - - +
357A GLY* 4.0 1.9 - - - -
358A TYR* 3.5 29.9 - - + -
371A PHE* 3.6 22.0 - - + -
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Residues in contact with ASP 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 ASN* 3.1 25.3 + - - +
346A SER* 3.5 11.8 - - - +
347A VAL 3.1 1.0 - - - -
348A ALA* 1.3 77.1 - - - +
350A THR* 1.3 63.4 + - - +
352A LYS* 3.1 20.7 + - - +
353A THR* 3.1 19.8 + - - +
358A TYR* 2.7 31.9 + - - -
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Residues in contact with THR 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 SER 3.1 13.6 + - - -
347A VAL* 3.6 12.2 - - - +
349A ASP* 1.3 74.9 - - - +
351A ASN* 1.3 68.3 + - - +
353A THR* 2.8 29.1 + - - +
354A LYS* 3.2 26.1 + - + +
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Residues in contact with ASN 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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307A GLN* 2.9 35.6 + - - +
343A ARG* 3.5 15.4 - - - +
347A VAL* 2.9 42.3 + - - +
348A ALA 3.6 3.4 - - - +
350A THR* 1.3 80.5 - - - +
352A LYS* 1.3 53.1 + - - +
354A LYS* 3.0 21.4 + - - +
355A GLY 3.2 0.3 + - - -
356A GLY* 2.7 28.8 + - - -
439A SER* 3.3 13.0 + - - -
580B TYR* 4.5 4.7 + - - -
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Residues in contact with LYS 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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310A VAL* 4.2 7.6 - - + +
311A GLY* 3.1 45.1 + - - +
312A PRO* 3.2 11.6 + - + +
314A ASP* 2.6 35.9 + - - -
348A ALA 3.0 14.3 + - - +
349A ASP* 3.2 22.7 - - - +
350A THR 3.1 0.4 - - - -
351A ASN* 1.3 76.3 - - - +
353A THR* 1.3 61.3 + - + +
355A GLY 3.0 10.0 + - - -
356A GLY 3.7 15.3 - - - +
357A GLY* 3.9 8.0 - - - +
358A TYR* 4.7 18.6 - - + +
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Residues in contact with THR 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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312A PRO* 4.1 13.1 - - + +
349A ASP 3.2 16.8 - - - +
350A THR* 2.8 19.6 + - - +
352A LYS* 1.3 77.3 - - + +
354A LYS* 1.3 61.8 + - - +
355A GLY 3.2 0.7 - - - -
581B GLU* 4.5 2.6 - - - +
583B HIS* 3.2 23.0 + - - -
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Residues in contact with LYS 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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350A THR* 3.2 28.7 + - + +
351A ASN* 3.0 15.8 + - - +
353A THR* 1.3 84.3 - - - +
355A GLY* 1.3 56.3 + - - +
356A GLY 3.4 1.6 - - - +
515B PHE* 6.0 0.2 - - - +
516B PRO* 4.7 13.5 - - - +
517B SER* 3.3 32.5 + - - +
578B VAL* 4.0 6.4 - - + +
580B TYR* 3.6 11.6 - - + -
581B GLU* 3.2 40.0 + - - +
583B HIS* 4.0 4.5 - - - -
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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