Contacts of the strand formed by residues 260 - 264 (chain A) in PDB entry 1ZGA
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 ALA 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.7 28.9 - - + -
202A SER 3.4 3.7 + - - +
203A LEU* 3.4 6.4 - - + -
204A VAL* 3.0 28.1 + - - +
258A ALA* 3.1 2.1 - - - +
259A ASP* 1.3 81.9 - - - +
261A VAL* 1.3 65.4 + - - +
286A ILE* 4.1 2.0 - - - -
294A LYS* 3.0 24.9 - - + +
296A ILE* 4.5 9.2 - - + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 5.3 0.4 - - - -
204A VAL* 3.6 17.3 - - + -
206A VAL* 3.7 25.1 - - + -
255A ILE* 4.5 1.6 - - + -
258A ALA 5.5 0.4 - - - +
260A ALA* 1.3 74.9 - - - +
262A LEU* 1.3 56.7 + - - +
263A LEU* 4.0 9.6 - - + -
282A SER* 3.4 46.9 - - - +
285A ALA* 3.8 11.9 - - + -
286A ILE* 3.7 11.7 - - + -
294A LYS 3.1 5.9 + - - -
295A VAL* 3.3 9.4 - - + +
296A ILE* 2.7 33.9 + - - +
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Residues in contact with LEU 262 (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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186A PHE* 4.8 5.4 - - + -
197A PHE* 5.2 5.2 - - + -
203A LEU* 4.1 15.7 - - + +
204A VAL 2.8 14.5 + - - +
205A ASP* 3.6 21.7 - - + +
206A VAL* 3.2 30.0 + - - +
213A VAL* 4.2 9.2 - - + -
217A ILE* 3.6 29.8 - - + -
260A ALA 4.1 0.8 + - - -
261A VAL* 1.3 73.4 - - - +
263A LEU* 1.3 64.4 + - - +
264A LYS* 4.0 11.7 + - + +
296A ILE* 3.5 24.0 - - + +
298A ILE* 4.0 26.2 - - + -
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Residues in contact with LEU 263 (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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206A VAL* 3.6 34.5 - - + -
261A VAL* 4.0 9.2 - - + -
262A LEU* 1.3 75.1 - - - +
264A LYS* 1.3 62.0 + - - +
265A TRP 3.7 1.4 + - - -
266A VAL* 4.4 19.8 + - + -
267A LEU* 3.8 22.1 + - + -
278A ILE* 3.9 19.1 - - + -
279A LEU* 3.8 28.5 - - + -
282A SER* 4.0 6.7 - - - +
295A VAL* 3.9 15.3 - - + -
296A ILE 2.7 13.1 + - - +
297A ILE* 3.6 8.8 - - + +
298A ILE 3.0 21.9 + - - +
299A ASP* 5.2 0.5 - - - +
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Residues in contact with LYS 264 (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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183A SER* 5.3 4.0 + - - +
186A PHE* 3.5 59.3 - - + +
205A ASP* 5.0 1.5 + - - +
206A VAL 4.9 1.0 + - - -
213A VAL* 3.9 13.9 - - + +
262A LEU* 3.8 19.2 + - + +
263A LEU* 1.3 71.1 - - - +
265A TRP* 1.3 114.1 + - + +
266A VAL* 3.0 5.4 + - - +
298A ILE* 3.9 11.9 - - + -
3994A SAH 2.8 53.8 + - - +
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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