Contacts of the strand formed by residues 315 - 322 (chain A) in PDB entry 2ZH1
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 PRO 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A PHE* 3.4 40.1 - - + +
308A LEU* 3.9 10.8 - - + -
309A GLU* 3.6 40.4 - - + +
313A PHE 3.6 2.0 - - - -
314A MET* 1.3 90.9 - - - +
316A LEU* 1.3 63.7 + - - +
317A ARG 5.5 0.4 - - - +
331A PHE* 6.0 0.4 - - + -
332A GLU 3.4 8.7 - - - +
333A CYS* 3.9 15.5 - - - -
334A GLN* 5.1 0.3 - - - +
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Residues in contact with LEU 316 (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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274A ARG* 4.3 7.0 - - - +
276A THR* 4.3 13.0 - - + -
305A PHE* 4.2 5.6 - - - -
314A MET 4.3 0.4 - - - +
315A PRO* 1.3 79.9 - - - +
317A ARG* 1.3 75.1 + - + +
332A GLU* 2.7 51.9 + - + +
333A CYS 4.7 0.2 - - - -
334A GLN* 3.4 39.3 - - + +
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Residues in contact with ARG 317 (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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237A ARG* 5.2 10.3 - - - +
305A PHE* 4.1 11.7 - - - -
315A PRO* 4.0 0.5 - - - +
316A LEU* 1.3 91.9 - - + +
318A SER* 1.3 64.5 + - - +
331A PHE* 3.8 2.8 - - - -
332A GLU* 3.5 24.3 + - - +
431A GLU* 3.0 38.7 + - - +
432A MET* 3.2 39.8 + - + +
433A MET 5.5 0.2 - - - -
434A GLY* 4.9 2.2 - - - +
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Residues in contact with SER 318 (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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301A SER* 3.9 18.6 + - - -
302A ARG* 5.6 0.5 - - - -
305A PHE* 4.1 13.8 - - - +
317A ARG* 1.3 80.2 + - - +
319A ALA* 1.3 65.9 + - - +
320A PHE* 5.8 0.2 - - - -
330A LEU 3.4 7.2 - - - -
331A PHE* 3.6 27.1 - - - -
432A MET* 3.8 6.6 - - - +
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Residues in contact with ALA 319 (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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301A SER* 3.6 8.0 + - - -
318A SER* 1.3 81.0 + - - +
320A PHE* 1.3 73.3 + - - +
329A LEU* 3.6 0.2 - - - -
330A LEU* 2.8 33.6 + - + +
428A GLU* 4.8 12.6 - - + +
432A MET* 3.8 23.6 - - + -
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Residues in contact with PHE 320 (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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294A TYR* 3.8 30.0 - + - -
297A LEU* 3.8 26.9 - - + -
298A GLU* 3.4 47.6 - - + -
301A SER* 3.4 24.0 - - - +
318A SER* 5.8 0.2 - - - -
319A ALA* 1.3 83.1 - - - +
321A LYS* 1.3 61.5 + - - +
328A TYR 3.0 13.9 - - - +
329A LEU* 4.0 8.7 - - + -
330A LEU* 3.9 3.1 - - - -
428A GLU* 4.1 9.0 - - - +
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Residues in contact with LYS 321 (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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294A TYR* 6.2 0.7 - - - -
297A LEU* 4.7 4.8 - - - +
320A PHE* 1.3 74.3 - - - +
322A ALA* 1.3 95.1 + - - +
323A SER* 3.9 11.2 - - - +
327A CYS* 3.4 4.3 - - - +
328A TYR* 2.9 33.3 + - + +
330A LEU* 4.2 0.6 - - + +
424A PRO* 3.4 22.9 + - - +
425A VAL* 4.3 16.6 - - + -
427A ALA* 6.0 0.4 - - - +
428A GLU* 3.2 41.7 + - + +
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Residues in contact with ALA 322 (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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285A LYS* 5.5 0.7 - - + -
293A LEU* 4.1 23.3 - - + -
294A TYR* 3.6 28.8 + - + +
297A LEU* 4.3 4.5 - - + -
321A LYS* 1.3 94.3 - - - +
323A SER* 1.3 64.6 + - - +
326A PHE 3.9 3.4 - - - -
327A CYS* 4.3 8.1 - - - -
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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