Contacts of the strand formed by residues 324 - 330 (chain A) in PDB entry 4Z2C
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A MET* 5.3 0.2 - - - +
239A VAL* 4.0 22.4 - - + +
240A LEU 3.2 16.8 - - - +
241A ARG* 2.9 43.5 + - - +
262A PRO* 4.8 0.2 - - - -
318A PHE* 3.3 37.9 + - + +
319A LYS* 5.7 0.8 - - - +
321A THR 3.5 14.6 + - - +
323A MET* 1.3 80.6 - - - +
325A THR* 1.3 63.7 + - - +
326A ASN* 5.8 0.2 - - - +
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Residues in contact with THR 325 (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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239A VAL* 3.7 3.1 - - - +
240A LEU* 2.9 36.2 + - - +
262A PRO* 3.9 17.9 - - - +
263A TYR 5.0 1.9 + - - -
265A VAL* 4.3 9.8 - - + +
322A GLN* 3.6 45.5 - - + +
324A GLN* 1.3 79.3 - - - +
326A ASN* 1.3 76.5 + - - +
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Residues in contact with ASN 326 (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 SER* 5.9 5.4 - - - -
238A ILE 3.5 10.7 - - - +
239A VAL* 4.0 17.0 - - - +
240A LEU* 4.8 3.0 - - - +
324A GLN* 5.8 0.2 - - - +
325A THR* 1.3 89.1 + - - +
327A PHE* 1.3 63.6 + - - +
328A GLY 4.4 0.3 + - - -
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Residues in contact with PHE 327 (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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179A ASN* 3.1 31.0 - - - -
180A ILE 3.8 0.4 - - - -
181A PRO* 3.4 48.9 - - + -
215A PHE* 4.3 16.6 - + - -
236A GLY 3.6 1.0 - - - +
237A SER* 3.4 5.2 - - - -
238A ILE* 2.9 48.3 + - + +
240A LEU* 4.1 16.4 - - + +
263A TYR* 4.3 17.9 - + - -
264A MET* 5.1 4.5 - - + -
326A ASN* 1.3 77.4 - - - +
328A GLY* 1.3 60.7 + - - +
329A PHE* 3.6 36.1 - + - -
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Residues in contact with GLY 328 (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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179A ASN* 3.4 23.2 + - - +
236A GLY 3.5 6.3 - - - -
237A SER* 4.6 3.8 - - - -
326A ASN 4.3 0.4 - - - -
327A PHE* 1.3 77.9 - - - +
329A PHE* 1.3 67.4 + - - -
330A ASN* 3.0 7.7 + - - +
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Residues in contact with PHE 329 (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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179A ASN 3.6 6.3 - - - -
181A PRO* 3.4 27.4 - - + -
213A PRO* 3.4 28.7 - - + -
227A ILE* 5.0 3.4 - - - -
230A ALA* 3.4 28.9 - - + -
231A TYR* 3.8 22.7 - + - -
234A GLY 3.6 5.4 - - - +
235A LYS* 3.1 7.4 - - - +
236A GLY 2.8 36.5 + - - +
238A ILE* 3.6 37.7 - - + -
327A PHE* 3.6 13.4 - + - -
328A GLY* 1.3 68.1 - - - +
330A ASN* 1.3 60.3 + - - +
331A MET* 4.2 15.3 - - + -
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Residues in contact with ASN 330 (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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177A ALA* 2.3 35.6 + - - +
178A THR* 3.4 2.4 + - - -
179A ASN* 2.9 29.1 + - + +
234A GLY 3.5 2.2 - - - -
235A LYS* 3.0 31.4 + - + +
328A GLY 3.0 7.4 + - - +
329A PHE* 1.3 73.0 - - - +
331A MET* 1.3 53.6 + - - +
332A LEU* 2.7 21.4 + - - +
341A ILE* 3.5 16.1 - - - +
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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