Contacts of the helix formed by residues 344 - 354 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B ARG* 1.3 77.4 - - - +
345B ASN* 1.3 66.1 + - - +
346B SER* 3.9 17.8 + - - +
347B VAL* 3.2 24.7 + - + +
348B ALA* 3.0 21.8 + - - +
371B PHE* 4.4 0.2 - - - -
373B GLU* 3.5 38.8 + - - +
374B ILE 3.9 4.9 + - - +
375B HIS* 3.6 49.0 + - + +
376B ASN* 4.6 1.4 + - - +
444B ARG* 5.7 0.3 + - - -
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Residues in contact with ASN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG 3.7 0.8 + - - -
344B GLN* 1.3 71.1 - - - +
346B SER* 1.3 62.0 - - - +
348B ALA* 3.4 3.1 + - - +
349B ASP* 3.1 35.6 + - - +
358B TYR* 4.4 2.4 + - - -
371B PHE* 3.4 41.5 - - + -
373B GLU* 3.0 18.5 + - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLN* 3.9 16.3 + - - +
345B ASN* 1.3 79.9 - - - +
347B VAL* 1.3 64.2 + - - +
349B ASP* 3.3 10.1 + - - +
350B THR* 3.1 29.0 + - - -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 4.4 16.6 - - + -
344B GLN* 3.2 37.0 + - + +
346B SER* 1.3 85.3 + - - +
348B ALA* 1.3 61.2 + - - +
350B THR* 3.2 8.3 + - - +
351B ASN* 2.8 47.5 + - - +
376B ASN* 5.9 10.3 - - + +
444B ARG* 4.8 9.2 - - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ARG* 3.8 26.4 - - - +
344B GLN 3.0 11.7 + - - +
345B ASN 3.6 3.1 - - - +
347B VAL* 1.3 79.1 - - - +
349B ASP* 1.3 56.9 + - - +
351B ASN* 3.4 3.3 + - - +
352B LYS* 2.9 25.3 + - - +
357B GLY* 4.1 3.6 - - - -
358B TYR* 3.7 17.5 - - + -
371B PHE* 3.6 31.0 - - + -
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Residues in contact with ASP 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ASN* 3.1 26.4 + - - +
346B SER* 3.5 12.3 - - - +
347B VAL 3.2 0.2 - - - -
348B ALA* 1.3 74.2 - - - +
350B THR* 1.3 63.2 + - - +
352B LYS* 3.2 12.5 + - + +
353B THR* 3.2 28.3 + - + +
358B TYR* 2.8 29.7 + - - -
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B SER 3.1 14.5 + - - -
347B VAL* 3.2 12.7 + - - +
349B ASP* 1.3 75.5 - - - +
351B ASN* 1.3 66.6 + - - +
353B THR* 2.9 26.4 + - - +
354B LYS* 3.3 26.3 + - + +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B GLN* 3.2 33.6 + - - +
343B ARG* 3.5 14.9 - - - +
347B VAL* 2.8 41.0 + - - +
348B ALA 3.5 5.8 - - - +
350B THR* 1.3 77.4 - - - +
352B LYS* 1.3 57.8 + - - +
354B LYS* 3.2 17.9 + - - +
355B GLY 3.4 0.3 + - - -
356B GLY* 2.7 29.8 + - - -
357B GLY 3.9 0.7 - - - -
439B SER* 3.3 13.8 + - - -
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 4.5 7.2 - - + -
311B GLY* 2.8 31.9 + - - +
312B PRO* 3.2 26.3 + - + +
314B ASP* 2.8 33.4 + - - -
348B ALA 2.9 14.4 + - - +
349B ASP* 3.3 15.9 - - - +
350B THR 3.2 0.4 - - - -
351B ASN* 1.3 76.5 - - - +
353B THR* 1.3 63.7 + - + +
355B GLY 3.1 11.4 + - - -
356B GLY 3.6 14.6 - - - +
357B GLY* 3.9 7.4 - - - +
358B TYR* 4.7 24.5 - - + +
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO* 4.1 23.7 - - + +
349B ASP 3.2 15.9 + - - +
350B THR* 2.9 19.4 + - - +
352B LYS* 1.3 76.4 - - + +
354B LYS* 1.3 61.4 + - - +
355B GLY 3.3 0.7 + - - -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B THR* 3.3 28.9 + - + +
351B ASN* 3.2 15.1 + - - +
352B LYS 3.0 1.4 - - - -
353B THR* 1.3 84.2 - - - +
355B GLY* 1.3 56.5 + - - +
356B GLY 3.6 1.1 - - - -
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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