Contacts of the strand formed by residues 319 - 325 (chain A) in PDB entry 4GJC
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 ARG 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A TYR* 3.4 55.2 + - + +
182A ILE 3.4 16.4 - - - +
183A ASN* 3.9 14.8 - - - +
184A LEU* 3.9 3.7 - - - +
190A TRP* 3.7 5.6 - - - -
314A ASP* 2.9 61.0 + - + +
317A ASN* 3.8 26.0 - - + +
318A ASN* 1.3 79.4 - - - +
320A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 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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180A HIS 3.8 1.2 - - - +
181A TYR* 3.3 4.1 - - - -
182A ILE* 2.9 37.7 + - - +
184A LEU* 3.7 21.1 - - + -
190A TRP* 3.7 30.1 - - + -
192A ILE* 4.0 10.8 - - + -
214A VAL* 3.8 27.8 - - + -
311A THR* 3.6 28.9 - - + -
312A GLU 3.3 3.8 - - - +
313A PHE* 3.9 7.4 - - + -
319A ARG* 1.3 77.2 - - - +
321A GLY* 1.3 61.0 + - - +
322A PHE* 3.7 22.9 - - + -
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Residues in contact with GLY 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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179A PHE* 3.6 10.3 - - - -
180A HIS 3.4 7.9 - - - -
181A TYR* 3.4 24.9 - - - -
310A TYR 3.8 0.3 - - - +
311A THR* 3.4 7.3 - - - +
312A GLU* 2.8 33.7 + - - +
320A ILE* 1.3 73.9 - - - +
322A PHE* 1.3 62.4 + - - -
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Residues in contact with PHE 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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178A ASN 3.9 1.4 - - - +
179A PHE* 3.4 3.3 - - - -
180A HIS* 3.0 33.7 + - - +
182A ILE* 3.6 31.9 - - + -
192A ILE* 4.1 6.1 - - + -
214A VAL* 3.9 20.9 - - + -
262A LEU* 3.9 17.7 - - + -
265A LYS* 5.8 0.2 + - - -
267A TYR* 3.6 32.6 + + + +
301A LEU* 4.7 0.2 - - + -
305A PHE* 3.5 27.8 - + - -
309A PHE* 4.0 8.7 - - + -
310A TYR 3.4 1.3 - - - -
311A THR* 3.2 37.2 - - + -
320A ILE* 3.7 16.6 - - + -
321A GLY* 1.3 75.3 - - - -
323A ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 323 (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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175A TYR* 3.8 29.4 - - + -
176A GLU 4.1 3.8 - - - +
178A ASN 4.1 15.0 - - - +
179A PHE* 3.7 19.3 - - + -
180A HIS* 5.9 0.7 - - - -
265A LYS* 5.8 2.2 - - - +
309A PHE* 3.3 9.5 - - - -
310A TYR* 2.8 30.6 + - - +
322A PHE* 1.3 76.9 - - - +
324A LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 324 (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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157A ARG* 6.0 0.9 - - - +
175A TYR* 3.2 2.9 - - - -
176A GLU* 2.9 65.2 + - + +
265A LYS* 5.5 5.1 - - - +
308A LYS* 3.7 34.8 - - + +
309A PHE* 4.0 21.2 - - + -
323A ALA* 1.3 69.8 - - - +
325A ALA* 1.3 67.7 + - - +
3B SER 5.1 0.4 - - - +
92B GLY* 4.1 17.5 - - - -
93B GLY* 4.5 3.4 - - - +
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Residues in contact with ALA 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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154A TYR* 4.5 13.2 - - + -
157A ARG* 4.6 8.5 + - - +
174A HIS 3.3 11.0 - - - +
176A GLU* 4.6 3.5 - - - +
306A ILE 4.6 0.7 - - - +
307A ARG 3.5 18.6 - - - +
308A LYS 2.9 21.9 + - - +
309A PHE 4.5 0.2 - - - -
310A TYR* 3.8 17.7 - - + +
323A ALA 3.4 2.2 + - - -
324A LEU* 1.3 82.5 - - - +
326A ARG* 1.4 62.4 + - - +
3B SER* 5.4 0.2 + - - -
5B ILE* 4.9 5.9 - - - +
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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