Contacts of the strand formed by residues 313 - 321 (chain O) in PDB entry 5C7O
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 SER 313 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250O VAL 3.4 13.2 - - - -
251O HIS* 3.2 12.8 - - - -
252O SER 3.1 18.4 + - - -
312O VAL* 1.3 70.5 - - - +
314O VAL* 1.3 63.5 + - - +
385O TRP* 3.6 8.9 - - - -
386O TYR* 2.8 58.7 + - - -
388O ASN* 2.9 17.8 + - - -
278P ILE* 4.7 1.8 - - - -
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Residues in contact with VAL 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248O THR 3.9 0.3 - - - +
249O THR* 3.3 4.2 - - - -
250O VAL* 2.9 56.3 + - + +
313O SER* 1.3 78.1 - - - +
315O VAL* 1.3 64.3 + - - +
383O ILE* 3.4 33.0 - - + -
384O SER 3.5 13.2 - - - +
385O TRP* 3.6 19.1 - - + -
386O TYR* 3.8 4.0 - - - -
278P ILE* 4.2 12.6 - - + -
305P PHE* 3.9 21.3 - - + -
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Residues in contact with VAL 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225O THR* 4.1 21.3 - - + +
228O CYS* 3.5 26.5 - - + -
229O LEU* 4.1 22.0 - - + +
232O LEU* 5.2 2.5 - - + -
247O MET* 4.1 20.9 - - + -
248O THR 3.7 2.7 - - - -
249O THR* 4.6 1.1 - - - -
314O VAL* 1.3 76.1 - - - +
316O ASP* 1.3 62.4 + - - +
317O LEU* 4.1 9.9 - - + +
382O LEU 4.8 0.9 - - - +
383O ILE* 3.3 7.1 - - - +
384O SER* 2.8 43.4 + - - +
386O TYR* 3.8 12.3 - - + +
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Residues in contact with ASP 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O LEU 3.8 1.6 - - - +
247O MET* 3.4 1.9 - - - -
248O THR* 2.7 53.8 + - + +
250O VAL* 5.6 1.3 - - + -
314O VAL 5.1 1.3 - - - +
315O VAL* 1.3 74.2 - - - +
317O LEU* 1.3 58.4 + - - +
318O THR* 3.8 1.6 + - - -
381O LYS* 2.8 33.9 + - - +
382O LEU 3.6 3.6 - - - -
383O ILE* 3.9 13.9 - - + -
248P THR* 2.5 36.0 + - - +
305P PHE* 3.7 13.1 - - + -
316P ASP* 5.7 0.2 - - - -
381P LYS* 5.2 1.6 + - - -
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Residues in contact with LEU 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229O LEU* 3.8 32.3 - - + -
232O LEU* 4.6 14.6 - - + -
233O ALA* 5.2 3.8 - - + -
236O ILE* 5.7 1.1 - - + -
242O ILE* 4.8 13.7 - - + -
245O GLY* 4.4 1.6 - - - -
246O LEU 3.8 18.6 - - - +
247O MET* 4.5 7.0 - - + +
300O LEU* 4.4 15.9 - - + -
315O VAL* 4.0 4.9 - - + -
316O ASP* 1.3 72.3 + - - +
318O THR* 1.3 68.1 + - - +
319O CYS* 3.8 22.3 + - + -
380O VAL 3.5 1.7 - - - +
381O LYS* 3.3 2.8 - - - -
382O LEU* 2.8 50.8 + - + +
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Residues in contact with THR 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245O GLY* 3.2 1.6 - - - -
246O LEU 2.8 42.1 + - - -
316O ASP* 3.8 1.6 + - - -
317O LEU* 1.3 69.9 - - - +
319O CYS* 1.3 61.6 + - - +
379O PHE* 3.7 29.4 - - + -
380O VAL 3.4 3.6 - - - -
381O LYS* 2.9 29.7 + - - +
246P LEU* 3.8 19.3 - - + -
318P THR* 3.7 29.0 + - + -
379P PHE* 3.9 3.9 - - - -
381P LYS* 4.8 1.0 + - - -
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Residues in contact with CYS 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236O ILE* 4.7 3.4 - - - -
242O ILE* 4.4 12.3 - - + -
244O GLU 3.3 11.4 - - - +
245O GLY* 4.1 5.6 - - - -
317O LEU* 4.2 24.2 - - + -
318O THR* 1.3 75.7 - - - +
320O ARG* 1.3 60.9 + - - +
321O LEU* 4.0 16.7 + - - +
378O ASN 3.8 0.3 - - - +
379O PHE* 3.5 9.3 - - - -
380O VAL* 3.0 54.4 + - - +
382O LEU* 4.2 10.1 - - - -
379P PHE* 5.0 0.2 - - - -
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Residues in contact with ARG 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242O ILE* 3.8 3.5 - - - -
243O VAL* 2.8 53.9 + - + +
244O GLU* 2.7 59.5 + - + +
319O CYS* 1.3 73.0 - - - +
321O LEU* 1.3 68.2 + - - +
378O ASN* 3.2 14.4 - - + +
379O PHE* 4.1 10.2 - - + -
244P GLU* 4.0 5.4 - - - +
320P ARG* 3.6 52.0 - - - +
379P PHE* 5.1 0.9 - - + -
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Residues in contact with LEU 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236O ILE* 3.5 30.1 - - + -
240O PHE* 4.1 10.3 - - + -
241O GLY 3.2 13.5 - - - +
242O ILE* 4.0 11.2 - - + -
243O VAL* 3.9 4.9 - - - +
319O CYS* 4.0 13.7 - - - +
320O ARG* 1.3 79.9 + - - +
322O ALA* 1.3 61.5 + - - +
323O GLN 3.5 12.3 - - - +
325O ALA* 3.3 30.1 - - + -
330O ILE* 4.5 4.3 - - + -
377O ASP 4.7 2.5 - - - +
378O ASN* 2.8 36.9 + - - +
380O VAL* 4.1 20.4 - - + -
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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