Contacts of the strand formed by residues 302 - 308 (chain A) in PDB entry 4PAR
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A THR* 3.3 2.9 - - - -
247A GLU* 2.9 47.8 + - + +
262A TRP* 3.5 42.0 - - + -
293A PHE* 4.8 2.2 - - + -
295A LYS 3.5 9.0 - - - +
300A ASP 3.1 6.9 - - - +
301A GLY* 1.3 71.2 - - - -
303A VAL* 1.3 59.2 + - - +
304A TRP* 3.8 11.9 - - + +
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Residues in contact with VAL 303 (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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244A THR* 4.8 12.8 - - - +
245A ILE 3.6 4.5 - - - +
246A THR* 4.2 17.3 - - + -
293A PHE* 3.5 5.1 - - - -
294A GLN* 2.8 45.7 + - + -
295A LYS* 3.5 30.8 + - + -
300A ASP* 4.6 8.7 - - + +
301A GLY 4.0 9.0 - - - +
302A ALA* 1.3 79.8 - - - +
304A TRP* 1.3 65.7 + - - +
305A LYS* 4.7 1.3 - - + +
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Residues in contact with TRP 304 (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 TRP* 4.4 12.0 - + - -
244A THR* 3.4 3.9 - - - -
245A ILE* 2.9 51.7 + - + +
247A GLU* 3.4 25.5 + - + +
262A TRP* 4.2 15.5 - + - -
266A PRO 4.2 11.2 - - - -
267A GLN 4.2 8.1 - - - -
269A ARG* 3.2 65.3 - - + -
291A TYR* 3.5 25.1 - - + -
292A GLU 3.3 7.0 - - - +
293A PHE* 3.5 45.1 - + + -
302A ALA* 3.8 13.1 - - + +
303A VAL* 1.3 79.2 - - - +
305A LYS* 1.3 59.3 + - - +
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Residues in contact with LYS 305 (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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243A LEU* 3.6 9.6 - - + +
244A THR* 4.6 7.4 - - + +
291A TYR* 3.2 2.1 - - - -
292A GLU* 2.5 41.8 + - - +
294A GLN* 3.5 41.5 - - + +
303A VAL* 4.1 3.0 + - + -
304A TRP* 1.3 74.4 - - - +
306A ARG* 1.3 75.6 + - - +
307A VAL* 3.4 15.8 + - + +
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Residues in contact with ARG 306 (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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114A SER* 6.3 0.2 - - - -
185A LEU* 3.3 26.9 - - - +
241A ASP 3.8 10.7 + - - -
242A GLY* 3.3 23.8 + - - +
243A LEU* 2.8 49.1 + - + +
288A MET 3.6 20.2 + - - -
289A GLY* 4.3 0.4 - - - -
290A LEU 3.8 4.5 - - - +
291A TYR* 3.5 20.2 + - + -
305A LYS* 1.3 84.4 + - - +
307A VAL* 1.3 60.3 + - - +
308A LYS 3.6 24.2 - - - +
309A SER* 4.4 10.1 + - - -
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Residues in contact with VAL 307 (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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268A LYS* 4.1 16.6 - - - +
290A LEU* 3.0 15.7 + - + +
291A TYR 4.6 0.4 - - - -
292A GLU* 3.6 41.7 - - + +
294A GLN* 5.6 1.1 - - - +
305A LYS* 3.4 19.9 + - + +
306A ARG* 1.3 75.0 - - - +
308A LYS* 1.3 76.3 + - + +
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Residues in contact with LYS 308 (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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268A LYS* 6.1 1.3 - - - +
289A GLY* 3.7 0.9 - - - -
290A LEU* 2.9 62.9 + - + +
306A ARG* 3.5 9.9 - - - +
307A VAL* 1.3 92.9 - - + +
309A SER* 1.3 61.2 + - - +
310A GLU* 3.3 25.5 + - - +
311A VAL* 5.4 0.9 - - - +
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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