Contacts of the strand formed by residues 308 - 319 (chain A) in PDB entry 5E9W
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 LEU 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A CYS* 5.7 0.4 - - - -
278A PHE* 3.4 25.3 - - + +
279A ASP 4.0 2.7 - - - -
280A ILE 4.0 4.0 - - - +
281A CYS* 3.7 15.7 - - + +
304A ALA 3.7 19.9 + - - +
305A CYS* 3.3 15.4 + - - +
306A GLU 3.3 2.6 - - - +
307A ARG* 1.3 77.2 - - - +
309A SER* 1.3 68.1 + - - +
310A PRO* 3.8 1.9 - - - +
312A GLY 4.5 1.3 - - - -
313A TYR 3.6 34.5 - - - +
314A PHE* 4.0 3.6 - - + +
387A MET* 3.8 29.8 - - + -
474A LYS* 3.2 22.7 - - + +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A CYS* 3.4 26.4 - - - +
278A PHE 3.0 15.4 + - - -
279A ASP* 4.6 11.0 + - - -
307A ARG 3.5 1.2 + - - -
308A LEU* 1.3 75.6 - - - +
310A PRO* 1.3 67.9 - - - +
311A GLY 3.3 0.2 + - - -
312A GLY* 2.8 31.2 + - - -
474A LYS* 3.4 4.4 - - - +
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Residues in contact with PRO 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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308A LEU 4.2 2.2 - - - +
309A SER* 1.3 90.5 - - - +
311A GLY* 1.3 58.5 + - - +
312A GLY 3.5 0.2 + - - -
474A LYS* 3.6 12.3 - - + +
475A GLN 3.9 13.2 - - - +
476A GLN* 3.7 40.7 - - - +
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Residues in contact with GLY 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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191A VAL* 5.3 1.0 - - - +
194A LYS* 2.8 40.1 + - - +
310A PRO* 1.3 71.0 - - - +
312A GLY* 1.3 63.4 + - - +
313A TYR* 3.4 10.9 - - - -
473A GLU* 3.7 5.3 - - - +
474A LYS 2.7 19.9 + - - -
475A GLN 4.9 0.2 - - - -
476A GLN* 5.3 0.6 - - - +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 5.4 0.9 - - - -
279A ASP* 3.2 21.8 - - - -
308A LEU* 4.5 5.6 - - - +
309A SER* 2.8 18.7 + - - -
310A PRO 3.2 1.0 + - - -
311A GLY* 1.3 80.9 - - - +
313A TYR* 1.3 60.3 + - - -
473A GLU* 3.4 3.1 - - - -
474A LYS* 2.8 27.9 + - - +
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Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 3.7 27.1 - + + -
190A LYS* 3.9 31.4 - - + +
191A VAL* 3.8 29.4 - - + -
194A LYS* 3.0 29.7 + - - -
279A ASP 2.9 10.1 + - - +
280A ILE* 3.2 7.4 - - + +
281A CYS 2.8 32.7 + - - +
308A LEU* 3.6 6.9 - - - +
311A GLY 3.4 12.8 - - - -
312A GLY* 1.3 72.2 - - - -
314A PHE* 1.3 56.2 + - - +
315A ILE* 3.9 15.9 - - + -
390A VAL* 4.0 11.9 - - + -
472A PHE 3.2 13.5 - - - +
473A GLU* 3.8 26.9 + - + -
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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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281A CYS* 3.6 10.5 - - - +
283A CYS* 4.0 21.5 - - + -
287A CYS* 4.0 12.8 - - - -
300A MET* 6.5 0.7 - - + -
301A LEU* 3.6 25.4 - - + -
304A ALA* 3.6 28.0 - - + -
305A CYS* 3.8 17.5 - - - -
308A LEU* 4.0 5.3 - - + +
313A TYR* 1.3 72.0 - - - +
315A ILE* 1.3 62.0 + - - +
378A LEU* 5.2 3.1 - - + -
382A ALA* 5.6 0.4 - - + -
387A MET* 3.8 17.9 - - + -
470A PHE* 3.6 28.8 - + - -
471A ALA* 3.2 1.9 - - - -
472A PHE* 2.6 63.2 + + + +
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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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183A LEU* 4.2 22.0 - - + +
184A ILE* 4.4 19.5 - - + -
187A PHE* 3.9 24.0 - - + -
215A TRP* 4.9 0.9 - - + -
280A ILE* 4.0 17.5 - - + -
281A CYS 3.0 14.7 + - - +
282A SER* 3.9 7.4 - - - +
283A CYS* 2.8 27.7 + - - +
284A GLN* 3.9 13.9 - - - +
313A TYR* 4.1 12.8 - - + +
314A PHE* 1.3 79.7 - - - +
316A GLY* 1.3 59.8 + - - +
470A PHE* 3.4 12.6 - - - +
471A ALA* 3.9 16.8 - - + -
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Residues in contact with GLY 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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183A LEU* 4.1 3.0 - - - +
283A CYS 3.0 13.2 - - - -
284A GLN* 3.8 8.7 - - - +
315A ILE* 1.3 77.4 - - - +
317A THR* 1.3 69.7 + - - +
469A VAL* 3.4 2.4 - - - +
470A PHE* 2.9 47.6 + - - +
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Residues in contact with THR 317 (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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179A MET* 6.0 2.2 - - + -
180A LYS* 5.3 4.0 - - + -
183A LEU* 4.6 4.9 - - + -
283A CYS 3.3 4.5 + - - +
284A GLN* 2.9 20.6 + - - +
285A PHE* 3.1 59.4 + - + -
286A VAL 4.1 1.9 + - - -
287A CYS* 5.0 1.2 + - - +
316A GLY* 1.3 79.4 - - - +
318A THR* 1.3 63.8 + - - +
395A PHE* 3.6 28.0 - - + -
467A TYR* 4.7 1.1 - - - -
468A LEU 3.4 6.1 - - - -
469A VAL* 3.9 11.2 - - + -
470A PHE* 3.8 1.8 - - - -
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Residues in contact with THR 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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287A CYS* 4.2 11.2 - - + +
288A HIS* 3.1 26.2 + - - +
317A THR* 1.3 76.9 - - - +
319A PRO* 1.3 88.3 - - - +
373A VAL* 3.9 20.8 - - + +
375A PHE* 5.4 1.6 - - + -
378A LEU* 5.4 2.7 - - + -
467A TYR* 3.3 7.7 - - - -
468A LEU* 3.0 41.8 + - + +
470A PHE* 4.2 11.9 - - + -
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Residues in contact with PRO 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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288A HIS* 3.3 18.4 - - + +
318A THR* 1.3 104.7 + - - +
320A ASN* 1.3 62.9 + - - +
321A SER 3.5 2.8 + - - -
324A LEU* 3.8 15.7 - - + -
358A TYR* 3.3 26.9 - - - +
360A PHE* 6.4 0.7 - - + -
370A GLU* 3.7 9.4 - - - +
373A VAL* 4.3 11.6 + - + +
466A ILE* 3.7 12.8 - - + +
467A TYR* 3.3 27.3 - - + +
468A LEU* 4.3 1.6 - - - +
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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