Contacts of the strand formed by residues 328 - 336 (chain A) in PDB entry 2V5Y
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 GLU 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A THR* 3.5 5.9 - - - -
303A ALA* 2.9 47.7 + - + +
326A ASP 4.4 0.2 + - - -
327A THR* 1.3 76.2 - - - +
329A TYR* 1.3 70.2 + - - +
330A GLU* 5.9 0.2 - - - +
351A ARG* 4.6 13.5 - - - +
352A THR* 4.4 5.9 + - - +
353A ARG* 3.7 36.4 + - + +
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Residues in contact with TYR 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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278A LEU* 4.3 7.9 - - + -
300A TYR* 4.1 17.4 - + + -
301A CYS 3.8 13.7 - - - -
302A THR* 3.6 27.8 - - + +
303A ALA* 5.3 0.4 - - - -
307A TRP* 5.8 4.0 - + - -
323A LEU* 3.4 38.5 - - + +
324A ASP* 3.1 46.6 + - - +
327A THR* 3.4 24.2 + - + -
328A GLU* 1.3 78.2 - - - +
330A GLU* 1.3 61.8 + - - +
331A ILE* 3.8 15.2 - - + +
351A ARG* 3.4 3.1 - - - -
352A THR 2.7 42.1 + - - +
354A THR* 3.8 9.4 - - + -
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Residues in contact with GLU 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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299A GLU 3.9 0.5 - - - +
300A TYR* 3.3 4.2 - - - +
301A CYS* 2.9 56.4 + - - +
302A THR 5.6 1.8 - - - -
303A ALA* 5.6 6.0 - - + +
328A GLU* 5.9 0.2 - - - +
329A TYR* 1.3 74.4 - - - +
331A ILE* 1.3 62.8 + - - +
332A SER* 4.4 0.8 + - - +
349A ALA* 4.0 22.7 - - + +
350A LEU 3.6 3.8 - - - -
351A ARG* 4.0 27.3 + - + -
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Residues in contact with ILE 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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268A PRO* 3.7 14.5 - - + +
278A LEU* 3.9 16.4 - - + -
280A ILE* 3.9 30.1 - - + -
298A VAL* 4.0 13.0 - - + -
299A GLU 3.4 7.9 - - - +
300A TYR* 3.9 6.3 - - + -
320A ILE* 3.9 19.1 - - + -
329A TYR* 3.8 19.5 - - + +
330A GLU* 1.3 90.2 - - - +
332A SER* 1.3 62.5 - - - +
349A ALA* 3.2 2.9 - - - -
350A LEU* 2.8 53.6 + - + +
352A THR* 5.1 1.6 - - - +
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Residues in contact with SER 332 (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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298A VAL* 4.0 0.9 - - - -
299A GLU* 3.0 57.4 + - - +
330A GLU* 4.3 1.3 - - - +
331A ILE* 1.3 76.2 - - - +
333A VAL* 1.3 65.0 + - - +
334A LEU* 4.8 0.2 - - - -
346A PRO* 3.8 12.7 - - - +
347A GLY 3.7 21.1 - - - -
348A PRO 4.1 5.8 - - - -
349A ALA* 4.3 8.5 - - - -
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Residues in contact with VAL 333 (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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264A PRO* 3.3 19.5 - - + +
268A PRO* 4.0 25.8 - - + -
280A ILE* 4.9 1.3 - - + -
282A LEU* 3.5 37.7 - - + -
283A ASN 5.6 0.2 - - - +
284A ALA* 3.9 24.5 - - + +
296A ARG* 5.3 2.2 - - + -
297A GLU 3.6 12.8 - - - +
298A VAL* 4.9 2.0 - - + -
331A ILE* 5.1 0.4 - - + -
332A SER* 1.3 78.4 - - - +
334A LEU* 1.3 71.3 + - - +
335A LEU* 4.7 2.9 - - + -
347A GLY* 3.1 23.3 + - - +
348A PRO 4.7 2.6 + - - -
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Residues in contact with LEU 334 (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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295A ALA 4.2 0.2 - - - +
296A ARG* 3.5 3.3 - - - +
297A GLU* 2.8 52.0 + - + +
299A GLU* 3.4 45.3 - - + +
310A ARG* 3.3 38.8 - - + +
332A SER 4.4 0.4 - - - +
333A VAL* 1.3 72.8 - - - +
335A LEU* 1.3 63.1 + - - +
336A THR* 5.0 0.4 - - - -
343A THR* 3.9 15.7 - - + -
344A GLY 4.2 7.6 - - - +
345A SER 4.6 3.4 - - - -
346A PRO* 3.8 24.9 - - + -
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Residues in contact with LEU 335 (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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262A PRO* 3.7 29.1 + - + +
264A PRO* 4.1 19.4 - - + +
284A ALA* 3.7 34.1 - - + +
287A ILE* 3.3 33.9 - - + -
293A ILE* 4.1 13.2 - - + -
295A ALA 3.8 1.1 - - - -
296A ARG* 3.8 30.5 - - + +
333A VAL* 4.1 2.4 + - + -
334A LEU* 1.3 73.1 - - - +
336A THR* 1.3 61.8 + - - +
343A THR* 2.5 34.8 + - - +
345A SER 4.8 2.8 + - - -
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Residues in contact with THR 336 (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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262A PRO* 4.2 2.5 - - - -
293A ILE* 3.4 4.9 - - - +
294A VAL* 2.8 39.4 + - + +
295A ALA* 2.9 31.8 + - + +
297A GLU* 4.4 7.8 + - - +
334A LEU 4.7 1.6 + - - -
335A LEU* 1.3 78.6 + - - +
337A ARG* 1.3 68.9 + - - +
339A GLY 5.9 0.2 - - - +
342A GLY* 3.7 3.6 - - - -
343A THR* 3.3 32.2 + - - +
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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