Contacts of the strand formed by residues 308 - 316 (chain A) in PDB entry 5E2Q
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 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.9 27.4 - - + -
30A GLU* 4.2 23.3 - - + +
33A TYR* 3.8 37.7 + - + -
34A ALA* 4.3 3.8 - - + -
37A LEU* 5.0 0.7 - - + -
274A GLN* 4.3 4.8 + - - +
303A ASP* 5.3 0.2 - - - +
306A PRO* 4.1 11.1 - - - +
307A ILE* 1.3 82.1 - - + +
309A GLU* 1.3 64.0 + - - +
310A SER* 4.0 1.4 + - - -
332A VAL* 3.7 29.8 - - + -
333A ALA 3.3 7.6 - - - +
334A VAL* 4.9 2.5 - - + -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A MET* 5.7 0.7 - - - +
300A TRP* 2.8 31.4 + - + +
303A ASP* 4.7 1.9 - - - +
306A PRO* 3.8 22.2 - - + +
307A ILE 3.9 2.0 + - - -
308A VAL* 1.3 73.3 - - - +
310A SER* 1.3 66.9 + - - +
331A PHE* 4.0 8.7 - - + +
332A VAL* 3.7 1.0 - - - -
333A ALA 2.9 32.1 + - - +
335A VAL* 4.2 11.8 - - + +
372A ASP* 4.7 1.9 - - - +
374A THR* 4.9 4.8 + - - +
376A LEU* 4.2 26.9 - - + -
405A LYS* 2.7 35.7 + - - +
407A VAL* 4.6 9.7 - - + +
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Residues in contact with SER 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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33A TYR* 4.0 8.1 + - - -
37A LEU* 3.4 33.0 - - - +
277A MET* 4.1 10.9 - - - +
278A LEU* 5.8 0.7 - - - +
281A TYR* 5.8 1.0 - - - -
300A TRP* 2.8 29.7 + - - -
308A VAL* 4.0 1.9 + - - -
309A GLU* 1.3 82.1 + - - +
311A TYR* 1.3 59.4 + - - +
331A PHE* 3.3 22.2 - - - -
332A VAL* 4.5 4.3 - - - -
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Residues in contact with TYR 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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281A TYR* 3.3 30.3 - + - -
293A HIS* 3.2 21.5 - + - -
297A SER* 2.8 23.8 + - - -
300A TRP* 3.9 25.4 - + + -
310A SER* 1.3 77.3 - - - +
312A ILE* 1.3 65.2 + - - +
315A ILE* 3.5 35.9 - - + +
329A GLU* 5.8 1.2 - - - +
330A GLY* 3.2 2.8 - - - -
331A PHE* 3.0 50.3 + + + +
392A ILE* 3.7 30.5 - - + -
393A PRO* 3.6 17.8 - - + +
394A ASN 5.1 0.5 + - - -
395A TYR* 3.9 2.9 - - - -
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Residues in contact with ILE 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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37A LEU* 5.2 2.7 - - + +
40A ALA* 4.0 31.9 - - + +
41A ALA* 4.1 7.6 - - + +
258A VAL* 4.2 11.9 - - + -
262A LEU* 4.6 11.4 - - + -
278A LEU* 5.8 0.7 - - + -
281A TYR* 4.0 24.7 - - + -
285A PHE* 3.9 10.7 - - + -
293A HIS* 2.8 24.3 + - - -
311A TYR* 1.3 83.6 - - - +
313A GLY* 1.3 63.0 + - - +
315A ILE* 3.9 7.3 - - - +
328A PHE* 3.7 21.5 - - + -
329A GLU 3.5 13.2 - - - +
330A GLY* 4.0 4.3 - - - -
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Residues in contact with GLY 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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285A PHE* 3.7 22.0 - - - -
293A HIS* 4.0 3.1 - - - -
312A ILE* 1.3 78.7 - - - +
314A PHE* 1.3 64.5 + - - -
315A ILE* 3.2 12.4 + - - +
328A PHE* 4.0 8.1 - - - -
329A GLU 2.9 33.3 + - - +
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Residues in contact with PHE 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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47A ALA* 5.3 0.7 - - + -
51A GLN* 3.7 17.9 - - - -
196A TYR* 3.4 42.1 - - + +
197A ASN* 3.7 16.6 - - + +
217A ALA* 3.5 31.2 - - + -
251A TYR* 3.8 19.1 - + - -
255A LEU* 4.8 6.1 - - + -
285A PHE* 4.6 14.8 - + - -
290A ILE* 5.8 2.1 - - + +
293A HIS* 5.1 2.9 + - - -
313A GLY* 1.3 69.9 - - - -
315A ILE* 1.3 66.5 - - - +
316A GLU 4.0 0.2 - - - -
326A GLY* 3.4 21.5 - - - +
327A GLU 3.6 5.6 - - - -
328A PHE* 3.5 38.8 - + + -
395A TYR* 5.5 2.4 + - - -
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Residues in contact with ILE 315 (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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196A TYR* 3.5 15.2 - - - -
293A HIS* 3.9 11.2 - - + -
311A TYR* 3.5 30.1 - - + +
312A ILE* 3.9 4.9 - - - +
313A GLY* 3.2 34.8 + - - +
314A PHE* 1.3 76.3 - - - +
316A GLU* 1.3 77.6 + - + +
327A GLU 3.4 4.6 + - - -
329A GLU* 3.6 25.8 - - + +
392A ILE* 3.9 18.2 - - + -
394A ASN* 3.0 31.5 + - + +
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Residues in contact with GLU 316 (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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315A ILE* 1.3 87.5 - - + +
317A SER* 1.3 59.6 + - - +
318A TYR* 3.5 26.5 + - + -
326A GLY* 3.3 1.8 - - - -
327A GLU* 3.0 34.1 + - + +
329A GLU* 3.5 17.1 + - - +
390A ILE* 4.0 7.6 - - - +
392A ILE* 4.0 0.2 - - - +
394A ASN* 3.2 19.2 + - - +
1B ASP* 3.0 41.0 + - - +
2B ARG* 3.5 29.5 - - - +
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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