Contacts of the strand formed by residues 347 - 354 (chain A) in PDB entry 2NZ2
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 GLY 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE 3.8 0.5 - - - +
226A GLU* 3.3 8.6 - - - +
227A PHE* 3.0 28.7 + - - +
297A ILE* 4.0 8.3 - - - +
346A GLU* 1.3 76.9 - - - +
348A LYS* 1.3 65.7 + - - -
364A GLU 3.3 12.3 - - - -
365A SER* 3.9 6.7 - - - -
366A PRO* 4.6 5.8 - - - -
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Residues in contact with LYS 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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224A GLU* 3.2 38.6 + - + +
225A ILE 3.3 4.0 - - - -
226A GLU* 4.1 30.9 + - + +
297A ILE* 4.0 1.8 - - - +
347A GLY* 1.3 78.9 - - - +
349A VAL* 1.3 63.9 + - - +
350A GLN* 4.0 3.3 + - - +
363A ARG* 3.1 7.4 - - - +
364A GLU* 2.8 61.1 + - + +
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Residues in contact with VAL 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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223A LEU 3.6 1.2 - - - +
224A GLU* 3.4 4.6 - - - -
225A ILE* 2.9 35.7 + - - +
227A PHE* 4.1 9.9 - - + -
293A ALA* 3.6 28.7 - - + +
296A ASP* 3.9 18.4 - - + +
297A ILE* 3.7 26.7 - - + +
348A LYS* 1.3 77.3 - - - +
350A GLN* 1.3 66.8 + - - +
351A VAL* 3.8 19.7 + - + +
360A ILE* 4.2 8.7 - - + -
362A GLY 3.6 11.4 - - - +
363A ARG* 4.4 2.0 - - + -
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Residues in contact with GLN 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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222A ILE* 4.9 9.0 - - + -
223A LEU 3.6 6.3 - - - +
224A GLU* 4.4 19.9 + - + +
238A VAL* 6.0 1.6 - - + -
348A LYS* 4.0 7.3 + - - +
349A VAL* 1.3 73.4 - - - +
351A VAL* 1.3 59.0 + - - +
360A ILE* 3.6 0.9 - - - -
361A LEU* 2.7 43.1 + - + +
362A GLY* 2.9 32.1 + - - +
363A ARG* 3.8 21.4 + - - +
364A GLU* 4.1 18.2 + - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ASP 3.8 0.2 - - - +
222A ILE* 3.4 6.6 - - - +
223A LEU* 3.0 55.6 + - + +
225A ILE* 4.0 21.8 - - + -
289A ILE* 4.5 7.0 - - + -
293A ALA* 4.3 12.8 - - + -
349A VAL* 3.9 13.0 - - + +
350A GLN* 1.3 78.4 - - - +
352A SER* 1.3 60.5 + - - +
353A VAL* 4.8 3.8 - - + -
358A VAL* 4.4 10.8 - - + -
359A TYR 3.1 8.1 - - - +
360A ILE* 3.7 26.9 - - + -
361A LEU* 3.7 5.2 - - - +
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Residues in contact with SER 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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220A PRO* 3.3 26.0 - - - +
221A ASP 3.5 4.4 + - - -
222A ILE* 4.5 5.1 - - - +
351A VAL* 1.3 74.5 - - - +
353A VAL* 1.3 64.0 + - - +
354A LEU* 4.0 2.2 - - - +
358A VAL* 3.3 5.8 - - - +
359A TYR* 2.7 52.7 + - - -
361A LEU* 3.9 25.6 - - - -
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Residues in contact with VAL 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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221A ASP 3.0 35.3 + - - +
223A LEU* 3.9 26.2 - - + -
257A VAL* 4.0 5.8 - - + +
258A ALA* 4.2 13.5 - - - -
261A HIS* 3.2 31.4 + - + -
263A VAL* 3.7 27.1 - - + -
289A ILE* 4.1 14.1 - - + -
351A VAL* 4.8 5.2 - - + -
352A SER* 1.3 78.0 + - - +
354A LEU* 1.3 62.1 + - - +
357A GLN 3.7 2.0 - - - -
358A VAL* 4.7 3.6 - - + +
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Residues in contact with LEU 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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217A PRO 3.7 16.2 - - - +
218A ASN 3.5 24.5 - - - +
219A THR 3.8 0.7 - - - +
220A PRO* 3.5 33.7 - - + -
261A HIS* 3.9 5.8 - - - +
352A SER* 4.0 3.5 - - - +
353A VAL* 1.3 75.5 - - - +
355A LYS* 1.3 82.7 + - + +
356A GLY 3.4 2.2 - - - -
357A GLN* 3.0 25.4 + - - +
359A TYR* 4.0 20.7 + - + +
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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