Contacts of the strand formed by residues 308 - 314 (chain A) in PDB entry 5EO3
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 ILE 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A VAL* 3.8 28.3 - - + +
302A ALA* 4.1 9.2 - - + -
303A ASN* 3.9 29.4 - - + +
306A MET 3.4 3.5 - - - +
307A ALA* 1.3 77.5 - - - +
309A ASP* 1.3 64.5 + - - +
310A THR 3.6 27.8 - - - +
311A LEU* 3.9 4.5 - - + +
336A VAL* 4.0 29.2 - - + -
339A ASN* 4.8 5.3 - - + +
340A ALA 4.7 0.3 - - - -
341A GLY* 3.9 12.1 - - - -
364A ALA* 4.0 13.9 - - + -
365A ILE 3.9 3.6 - - - +
366A LEU* 4.2 8.1 - - + +
367A ARG* 4.0 12.4 + - - -
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Residues in contact with ASP 309 (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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284A MET* 5.6 0.3 - - - +
291A ARG* 4.9 5.0 + - - -
308A ILE* 1.3 72.3 - - - +
310A THR* 1.3 85.3 + - - +
341A GLY* 3.6 4.2 - - - -
342A THR* 3.1 23.9 + - - -
365A ILE* 2.7 32.2 + - - +
366A LEU 3.8 2.8 - - - +
367A ARG* 3.5 39.1 + - + +
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Residues in contact with THR 310 (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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277A ALA* 4.8 4.3 - - + -
308A ILE* 3.7 5.4 - - - -
309A ASP* 1.3 98.8 + - - +
311A LEU* 1.3 72.1 - - - +
312A LEU* 3.6 15.6 - - + +
342A THR* 3.2 15.9 - - - +
344A ARG* 3.9 31.2 + - + +
364A ALA* 3.2 6.2 - - - +
365A ILE* 2.9 37.0 + - - +
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Residues in contact with LEU 311 (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 VAL* 3.5 32.3 - - + -
308A ILE* 3.9 5.3 - - + +
310A THR* 1.3 78.1 - - - +
312A LEU* 1.3 64.1 + - - +
313A ILE* 4.5 7.4 - - + -
332A LEU* 4.2 16.8 - - + -
333A VAL* 4.3 12.3 - - + -
336A VAL* 4.2 23.8 - - + -
342A THR 2.8 11.7 + - - +
343A VAL* 3.6 27.3 - - + -
344A ARG* 2.9 27.2 + - - -
362A VAL* 3.9 13.7 - - + -
363A ALA 3.7 10.8 - - - +
364A ALA* 4.5 1.3 - - + +
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Residues in contact with LEU 312 (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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277A ALA* 4.3 4.9 - - + +
278A LEU* 3.9 38.4 - - + +
281A PHE* 4.5 7.2 - - + -
310A THR* 3.6 30.1 - - + +
311A LEU* 1.3 75.1 - - - +
313A ILE* 1.3 60.3 + - - +
344A ARG* 3.7 4.3 - - + -
346A PHE* 3.8 28.3 - - + -
356A LEU* 3.9 12.0 - - + +
361A GLY 3.8 0.3 - - - +
362A VAL* 3.4 4.9 - - - +
363A ALA* 2.8 42.4 + - + +
364A ALA* 4.3 1.6 - - - +
365A ILE* 4.1 21.5 - - + +
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Residues in contact with ILE 313 (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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311A LEU* 4.5 9.0 - - + -
312A LEU* 1.3 74.6 - - - +
314A SER* 1.3 66.8 + - - +
317A LEU* 4.0 9.9 - - + -
318A PHE* 3.8 26.5 - - + -
329A TYR* 4.0 26.9 - - + +
332A LEU* 5.2 1.6 - - + -
333A VAL* 4.4 10.5 - - + -
343A VAL* 4.2 12.6 - - + -
344A ARG 3.0 11.1 + - - +
345A ILE* 3.3 26.0 - - + -
346A PHE* 2.8 24.8 + - - -
356A LEU* 3.8 5.3 - - - +
361A GLY 3.4 8.5 - - - +
362A VAL* 4.0 13.2 - - + -
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Residues in contact with SER 314 (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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313A ILE* 1.3 73.3 - - - +
315A ASP* 1.3 62.9 + - - +
316A GLU* 3.9 17.6 + - - +
317A LEU* 3.2 18.9 + - - +
318A PHE* 3.8 6.7 - - - -
346A PHE* 3.7 12.7 + - - +
347A SER 4.8 0.7 + - - -
348A SER* 4.3 7.8 - - - -
353A GLY 4.3 5.5 + - - -
356A LEU* 3.7 7.0 - - - +
357A SER* 3.3 24.1 + - - -
361A GLY* 2.9 25.8 + - - -
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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