Contacts of the strand formed by residues 324 - 331 (chain A) in PDB entry 3I58
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 VAL 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A HIS* 5.9 0.7 - - + -
157A ASP* 3.7 26.9 - - + +
158A TYR* 3.4 33.7 - - + -
161A ILE* 6.1 0.2 - - + -
273A ILE* 4.3 3.4 - - + -
274A GLU* 3.8 10.5 - - - -
275A ALA* 4.0 16.2 - - + +
279A ASP* 3.4 9.8 - - - +
281A HIS* 5.0 1.1 - - + -
320A PRO* 3.6 2.9 - - - +
321A ILE* 2.8 36.9 + - + +
322A SER 4.1 1.9 - - - +
323A TYR* 1.3 84.8 - - + +
325A SER* 1.3 74.9 + - - +
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL 3.7 1.0 - - - +
273A ILE* 3.4 6.8 - - - +
274A GLU 3.2 27.5 + - - +
276A VAL* 3.9 22.2 - - - +
279A ASP* 3.2 23.4 + - - -
301A LEU* 6.2 0.7 - - - -
318A ALA* 5.4 4.0 - - - -
319A HIS 3.5 12.8 - - - -
320A PRO* 4.1 7.4 - - - +
321A ILE 4.1 0.9 - - - +
324A VAL* 1.3 78.7 + - - +
326A ILE* 1.3 65.3 + - - +
327A VAL* 4.0 4.4 - - - +
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Residues in contact with ILE 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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161A ILE* 3.3 29.6 - - + -
165A TYR* 3.9 31.9 - - + -
167A TRP* 4.4 5.4 - - + -
271A LEU* 4.3 26.9 - - + -
272A VAL 3.6 3.1 - - - -
273A ILE* 3.9 23.6 - - + -
318A ALA* 3.3 2.4 - - - -
319A HIS* 2.8 41.1 + - + +
321A ILE* 3.3 26.0 - - + -
325A SER* 1.3 75.0 - - - +
327A VAL* 1.3 60.7 + - - +
328A GLU 4.9 0.2 - - - +
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Residues in contact with VAL 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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270A VAL 3.7 1.0 - - - +
271A LEU* 3.5 3.1 - - - -
272A VAL* 2.9 38.2 + - + +
274A GLU* 6.0 0.7 - - + +
276A VAL* 4.5 11.9 - - + -
301A LEU* 3.9 26.2 - - + -
304A LEU* 4.1 17.5 - - + -
315A VAL* 4.5 8.1 - - + -
317A ALA 3.5 10.5 - - - +
318A ALA* 4.1 2.9 - - + +
325A SER* 4.8 2.0 - - - +
326A ILE* 1.3 79.5 - - - +
328A GLU* 1.3 58.2 + - - +
329A MET* 3.5 35.7 - - + -
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Residues in contact with GLU 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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165A TYR* 2.5 37.8 + - + -
269A VAL* 3.7 22.8 - - + +
270A VAL 3.6 2.9 - - - -
271A LEU* 3.7 16.2 - - + -
315A VAL* 3.5 2.4 - - - -
316A ARG* 2.8 37.0 + - + +
317A ALA* 3.2 30.7 + - + +
319A HIS* 4.3 7.1 + - - +
326A ILE* 3.8 1.7 + - + +
327A VAL* 1.3 72.5 - - - +
329A MET* 1.3 59.7 + - - +
330A THR* 4.7 7.0 - - + -
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Residues in contact with MET 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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257A LEU* 4.0 19.7 - - + -
269A VAL* 3.7 1.0 - - - +
270A VAL* 2.7 46.2 + - + +
272A VAL* 3.6 23.6 - - + -
304A LEU* 4.1 22.2 - - + +
308A ALA* 3.8 26.5 - - + -
313A LEU* 4.1 16.4 - - + -
314A ALA 3.3 9.6 - - - +
315A VAL* 4.3 13.7 - - + +
327A VAL* 3.5 28.5 - - + +
328A GLU* 1.3 77.0 - - - +
330A THR* 1.3 67.5 + - - +
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Residues in contact with THR 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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268A GLY 4.2 10.5 - - - +
269A VAL* 3.9 22.7 - - + -
270A VAL* 5.0 0.4 - - - +
313A LEU* 3.3 10.4 - - - +
314A ALA* 3.0 25.7 + - - +
316A ARG* 3.0 44.1 + - + +
328A GLU* 4.7 6.7 - - + -
329A MET* 1.3 78.0 - - - +
331A ALA* 1.3 68.0 + - - +
332A LEU 3.3 0.3 + - - -
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Residues in contact with ALA 331 (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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265A GLY 4.1 7.8 + - - +
266A SER* 4.0 30.3 - - - +
268A GLY 4.8 3.8 + - - -
312A GLY 3.9 4.9 - - - -
313A LEU* 3.9 6.7 - - - +
316A ARG* 2.9 16.1 + - - -
330A THR* 1.3 74.8 + - - +
332A LEU* 1.3 67.8 + - - +
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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