Contacts of the strand formed by residues 317 - 323 (chain A) in PDB entry 2P80
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.1 5.1 - - - -
225A GLY* 5.1 6.2 + - - -
227A LEU 5.6 0.2 + - - -
228A THR* 2.9 16.9 - - - +
302A ALA* 5.5 0.4 - - + -
304A VAL* 2.8 24.9 - - + -
311A ALA 3.2 21.1 - - - +
312A PHE* 5.0 10.5 - - + -
315A GLY 3.4 6.1 + - - +
316A ALA* 1.3 73.5 - - - +
318A ALA* 1.3 60.8 + - - +
319A HIS* 3.8 10.4 + - - +
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Residues in contact with ALA 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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178A VAL* 5.7 1.1 - - + -
220A PHE* 4.1 8.9 - - + -
227A LEU* 3.2 36.3 - - + -
228A THR* 3.2 7.0 - - - -
233A MET* 4.3 7.9 - - + -
302A ALA* 3.7 0.2 - - - +
303A TYR* 3.0 32.9 + - + +
317A ALA* 1.3 72.6 - - - +
319A HIS* 1.3 83.5 + - - +
320A PHE* 4.5 4.7 - - + -
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Residues in contact with HIS 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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227A LEU 2.9 7.9 + - - -
228A THR* 2.7 39.6 - - + +
229A GLY 4.2 3.2 + - - +
232A ALA* 2.5 39.3 - - + +
233A MET 3.1 3.3 + - - -
300A ILE* 3.8 24.3 - - + +
301A TYR 3.2 9.2 - - - +
302A ALA* 3.5 22.0 - - + +
312A PHE* 5.9 3.4 - - - -
317A ALA* 3.8 13.3 + - - +
318A ALA* 1.3 96.3 + - - +
320A PHE* 1.3 62.4 + - - +
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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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176A TYR* 4.3 8.3 - + - -
178A VAL* 4.9 6.1 - - + -
233A MET* 2.5 67.1 - - + -
234A THR* 4.2 8.5 - - - +
235A ALA* 5.4 0.4 - - + -
241A VAL* 5.6 2.2 - - + -
243A ILE* 4.6 24.2 - - + -
256A LEU* 4.8 4.0 - - + -
295A PHE* 4.7 19.7 - + + -
299A GLY 3.6 2.8 - - - +
300A ILE* 3.6 1.2 - - - -
301A TYR* 2.7 38.3 + - + +
303A TYR* 3.8 30.1 - + + -
318A ALA* 4.5 5.8 - - + -
319A HIS* 1.3 78.4 - - - +
321A LYS* 1.3 61.5 + - - +
322A VAL* 3.7 13.2 + - + +
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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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229A GLY 3.0 27.9 + - - -
230A ASP* 4.1 17.2 + - - +
232A ALA* 3.5 17.8 + - + -
233A MET 3.4 9.0 + - - +
234A THR* 3.3 14.0 - - + +
235A ALA 3.1 20.3 + - - -
299A GLY 3.8 4.5 - - - -
300A ILE* 3.8 24.5 - - + +
320A PHE* 1.3 71.2 - - - +
322A VAL* 1.3 59.6 + - - +
323A THR* 4.3 4.8 + - + +
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Residues in contact with VAL 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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235A ALA* 2.5 38.8 - - + +
236A ALA* 3.5 9.6 - - - -
237A VAL 3.6 9.4 - - - +
295A PHE* 3.8 34.8 - - + -
297A GLN 4.0 15.0 - - - +
298A PRO* 3.5 3.4 - - + +
299A GLY* 3.0 37.4 + - - +
301A TYR* 4.6 4.5 - - + -
320A PHE* 3.9 11.7 - - + +
321A LYS* 1.3 79.8 - - - +
323A THR* 1.3 65.8 + - - +
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Residues in contact with THR 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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235A ALA 3.1 5.0 + - - +
236A ALA* 3.2 16.7 - - - +
237A VAL* 2.9 24.9 + - - +
298A PRO* 3.8 4.3 - - - -
321A LYS* 5.3 4.3 - - + +
322A VAL* 1.3 80.6 - - - +
324A GLY* 1.3 58.3 + - - +
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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