Contacts of the helix formed by residues 305 - 314 (chain F) in PDB entry 1NZB
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 SER 305 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305E SER* 6.0 0.7 - - - -
307E PRO* 5.1 4.3 - - - -
303F GLY 3.6 2.6 + - - -
304F VAL* 1.3 79.8 - - - +
306F ILE* 1.3 64.2 + - - +
307F PRO* 3.2 15.8 - - - +
308F GLU* 3.1 31.0 + - - +
309F ILE* 3.0 22.7 + - - +
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Residues in contact with ILE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ILE* 3.7 26.5 - - + -
307E PRO* 3.9 28.1 - - + +
310E MET* 4.7 4.5 - - - -
318E VAL* 5.4 5.2 - - + -
305F SER* 1.3 73.5 - - - +
307F PRO* 1.3 73.5 - - + +
309F ILE* 3.0 9.5 + - + +
310F MET* 3.0 50.0 + - + +
318F VAL* 3.6 33.7 - - + -
321F VAL* 6.0 1.8 - - + -
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Residues in contact with PRO 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F SER* 3.2 17.9 - - - +
306F ILE* 1.3 95.8 - - + +
308F GLU* 1.3 57.7 + - + +
310F MET* 3.0 16.4 - - + +
311F GLN* 3.0 29.6 + - - +
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Residues in contact with GLU 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLY* 5.2 3.1 - - - -
334A ALA* 4.5 12.4 + - + +
337A ARG* 3.2 37.0 + - - -
299F MET* 4.7 0.7 - - - +
304F VAL* 3.7 16.4 - - + +
305F SER* 3.1 21.6 + - - +
307F PRO* 1.3 76.3 - - + +
309F ILE* 1.3 65.6 + - - +
310F MET 2.9 1.6 - - - -
311F GLN* 3.8 9.6 - - + +
312F ALA* 3.1 23.9 + - - +
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Residues in contact with ILE 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E PRO* 4.6 11.0 - - + -
296F ALA* 4.8 4.9 - - - +
299F MET* 4.2 21.5 - - + -
300F ALA* 3.8 34.3 - - + +
304F VAL* 3.5 30.3 - - + +
305F SER 3.0 15.8 + - - +
306F ILE* 3.8 7.0 - - + +
308F GLU* 1.3 76.2 - - - +
310F MET* 1.3 65.2 + - - +
312F ALA* 3.6 1.9 - - - +
313F GLY 3.3 12.3 + - - -
315F TRP* 3.4 18.4 - - + -
321F VAL* 4.1 26.9 - - + -
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Residues in contact with MET 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F ILE* 3.0 42.8 + - + +
307F PRO* 3.0 17.9 - - + +
309F ILE* 1.3 75.8 - - - +
311F GLN* 1.3 69.5 + - - +
313F GLY 2.9 14.0 + - - -
314F GLY* 3.0 10.7 + - - -
315F TRP* 3.4 38.1 + - + +
316F THR* 3.7 15.3 - - - +
317F ASN 3.0 25.1 - - - +
318F VAL* 4.7 7.4 - - + -
321F VAL* 5.5 3.6 - - - -
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Residues in contact with GLN 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F VAL* 5.9 4.6 - - - +
211F LYS* 4.1 8.1 + - - -
307F PRO 3.0 13.6 + - - +
308F GLU* 3.8 9.6 - - + +
310F MET* 1.3 78.8 - - - +
312F ALA* 1.3 65.7 + - - +
314F GLY* 3.3 10.1 + - - +
315F TRP 5.6 0.2 - - - -
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Residues in contact with ALA 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ALA* 5.5 2.9 - - + +
335A MET* 4.5 11.9 - - + +
170F THR 3.6 7.3 - - - +
171F LEU* 4.3 3.2 - - + +
211F LYS* 3.4 24.0 - - - +
299F MET* 3.7 31.0 - - + -
308F GLU 3.1 14.3 + - - +
309F ILE 3.6 7.0 - - - +
310F MET 2.9 1.2 + - - -
311F GLN* 1.3 81.9 - - - +
313F GLY* 1.3 56.6 + - - +
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Residues in contact with GLY 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F LEU* 3.8 13.5 - - - -
173F ARG* 5.4 2.4 + - - -
211F LYS* 5.0 3.1 - - - -
292F ARG* 3.5 24.2 + - - -
309F ILE 3.3 4.4 + - - -
310F MET 2.9 6.7 + - - -
312F ALA* 1.3 76.5 - - - +
314F GLY* 1.3 63.2 + - - +
315F TRP* 3.2 26.4 - - - -
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Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ARG* 5.4 4.5 + - - -
202F THR* 4.8 7.8 + - - -
211F LYS* 4.7 6.0 - - - +
310F MET 3.0 6.6 + - - -
311F GLN* 3.3 10.4 + - - -
312F ALA 3.4 0.4 + - - -
313F GLY* 1.3 79.8 - - - +
315F TRP* 1.3 65.4 + - - +
316F THR* 4.9 0.5 + - - -
116G T 5.1 0.7 - - - +
117G G 4.0 6.6 + - - -
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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