Contacts of the strand formed by residues 313 - 321 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278O ILE* 4.7 1.8 - - - -
250P VAL 3.4 12.8 - - - -
251P HIS* 3.3 12.4 + - - -
252P SER 3.1 19.2 + - - -
312P VAL* 1.3 70.2 - - - +
314P VAL* 1.3 64.2 + - - +
385P TRP* 3.6 9.5 - - - -
386P TYR* 2.8 58.4 + - - -
388P ASN* 2.9 17.6 + - - -
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Residues in contact with VAL 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278O ILE* 4.3 5.8 - - + -
305O PHE* 3.9 22.2 - - + -
248P THR 3.9 0.5 - - - +
249P THR* 3.3 3.3 - - - -
250P VAL* 2.9 56.4 + - + +
313P SER* 1.3 77.7 - - - +
315P VAL* 1.3 64.0 + - - +
316P ASP* 5.0 0.6 - - + +
383P ILE* 3.4 32.8 - - + -
384P SER 3.4 13.7 - - - +
385P TRP* 3.6 26.5 - - + -
386P TYR* 3.8 5.2 - - - -
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Residues in contact with VAL 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225P THR* 4.1 21.5 - - + +
228P CYS* 3.6 27.1 - - + -
229P LEU* 4.0 21.8 - - + +
232P LEU* 5.1 3.4 - - + -
247P MET* 4.0 21.8 - - + -
248P THR 3.7 2.5 - - - -
249P THR* 4.6 1.1 - - - -
314P VAL* 1.3 76.4 - - - +
316P ASP* 1.3 64.3 + - - +
317P LEU* 4.1 9.9 - - + +
382P LEU 4.8 0.9 - - - +
383P ILE* 3.3 6.6 - - - +
384P SER* 2.8 41.2 + - - +
386P TYR* 3.8 11.0 - - + +
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Residues in contact with ASP 316 (chain P).
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* 2.5 38.8 + - - +
305O PHE* 3.8 11.3 - - + -
316O ASP* 6.4 0.2 - - - -
381O LYS* 5.3 1.5 + - - -
246P LEU 3.8 1.7 - - - +
247P MET* 3.4 2.1 - - - -
248P THR* 2.7 54.0 + - + +
250P VAL* 5.7 1.8 - - + -
314P VAL 5.0 1.6 - - - +
315P VAL* 1.3 74.8 - - - +
317P LEU* 1.3 58.4 + - - +
318P THR* 3.8 1.6 + - - -
381P LYS* 2.8 30.9 + - - +
382P LEU 3.6 2.9 - - - -
383P ILE* 3.8 14.4 - - + -
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Residues in contact with LEU 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229P LEU* 3.8 33.4 - - + -
232P LEU* 4.5 15.7 - - + -
233P ALA* 5.0 10.5 - - + -
236P ILE* 5.5 2.0 - - + -
242P ILE* 5.0 7.4 - - + -
245P GLY* 4.6 1.8 - - - -
246P LEU 3.8 14.6 - - - +
247P MET* 4.5 6.1 - - + +
300P LEU* 4.4 20.4 - - + -
315P VAL* 4.0 4.7 - - + -
316P ASP* 1.3 72.4 + - - +
318P THR* 1.3 67.9 + - - +
319P CYS* 3.8 21.4 + - + -
380P VAL 3.6 1.9 - - - +
381P LYS* 3.3 1.2 - - - -
382P LEU* 2.8 52.8 + - + +
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Residues in contact with THR 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O LEU* 3.7 20.2 - - + -
318O THR* 3.7 26.9 + - + -
379O PHE* 4.0 3.9 - - - -
381O LYS* 5.0 1.0 + - - -
245P GLY* 3.2 1.7 - - - -
246P LEU 2.8 42.6 + - - -
316P ASP* 3.8 1.6 + - - -
317P LEU* 1.3 71.4 - - - +
319P CYS* 1.3 61.3 + - - +
379P PHE* 3.7 29.2 - - + -
380P VAL 3.4 2.7 - - - -
381P LYS* 2.9 29.9 + - - +
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Residues in contact with CYS 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379O PHE* 5.1 0.2 - - - -
236P ILE* 4.6 3.1 - - - -
242P ILE* 4.5 8.1 - - + -
244P GLU 3.3 11.0 - - - +
245P GLY* 4.1 5.2 - - - -
317P LEU* 4.2 23.6 - - + -
318P THR* 1.3 75.2 - - - +
320P ARG* 1.3 62.1 + - - +
321P LEU* 3.9 21.3 + - + +
378P ASN 3.9 0.2 - - - +
379P PHE* 3.5 9.8 - - - -
380P VAL* 3.0 54.6 + - - +
382P LEU* 4.2 11.9 - - - -
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Residues in contact with ARG 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244O GLU* 3.8 11.4 - - - +
320O ARG* 3.6 47.2 - - - +
379O PHE* 5.1 1.7 - - + -
242P ILE* 3.7 1.7 - - - +
243P VAL* 2.8 49.1 + - + +
244P GLU* 2.7 57.5 + - + +
319P CYS* 1.3 74.3 - - - +
321P LEU* 1.3 68.8 + - - +
378P ASN* 3.3 13.2 - - + +
379P PHE* 4.2 9.1 - - + -
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Residues in contact with LEU 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236P ILE* 3.6 29.8 - - + -
240P PHE* 4.1 11.4 - - + -
241P GLY 3.3 12.8 - - - +
242P ILE* 4.0 8.1 - - + -
243P VAL* 4.0 4.9 - - - +
319P CYS* 3.9 17.3 - - - +
320P ARG* 1.3 84.6 - - - +
322P ALA* 1.3 60.4 + - - +
323P GLN 3.9 11.7 - - - +
325P ALA* 3.3 28.3 - - + -
330P ILE* 4.6 2.7 - - + -
377P ASP 4.8 0.4 - - - +
378P ASN* 2.9 38.1 + - - +
380P VAL* 4.0 23.1 - - + -
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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