Contacts of the strand formed by residues 265 - 270 (chain G) in PDB entry 3SRF
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 LYS 265 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G ASP 3.1 8.9 + - - +
238G MET* 3.2 5.5 - - + +
239G VAL* 2.8 27.4 + - - +
263G ASN* 4.9 5.1 + - - +
264G ILE* 1.3 74.5 - - - +
266G ILE* 1.3 60.7 + - - +
267G ILE* 4.0 2.2 - - + -
287G ASP* 3.3 29.6 + - + +
438G HIS* 5.4 10.8 - - - -
461G GLN* 3.4 33.4 - - + +
464G LEU* 4.1 27.8 - - + -
465G TYR* 5.0 14.3 + - - +
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Residues in contact with ILE 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G VAL* 3.7 9.4 - - + +
241G ALA* 4.6 9.2 - - + -
250G VAL* 4.1 13.7 - - + +
253G VAL* 3.9 20.2 - - + -
254G ARG* 3.6 63.5 - - + +
257G LEU* 3.8 19.5 - - + -
264G ILE 4.2 0.4 - - - +
265G LYS* 1.3 74.1 - - - +
267G ILE* 1.3 64.8 + - - +
268G SER* 3.9 15.4 + - - +
286G SER* 4.0 0.3 - - - -
287G ASP* 2.8 36.4 + - - +
288G GLY 3.2 6.1 + - - +
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Residues in contact with ILE 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G MET* 4.6 8.5 - - + -
239G VAL 2.7 9.4 + - - +
240G PHE* 3.2 32.0 - - + +
241G ALA 3.1 21.6 + - - -
265G LYS* 4.5 4.3 - - + -
266G ILE* 1.3 75.2 - - - +
268G SER* 1.3 61.0 + - - +
269G LYS* 3.5 0.5 + - - +
287G ASP 4.3 3.8 - - - +
288G GLY* 3.5 23.8 - - - +
289G ILE 3.7 29.4 - - - +
290G MET* 3.7 7.4 - - + +
322G PRO* 5.1 2.2 - - + +
324G ILE* 3.8 18.6 - - + -
464G LEU* 3.8 33.9 - - + -
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Residues in contact with SER 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G ALA* 4.2 2.7 - - - +
244G ILE* 3.8 21.3 - - - +
250G VAL* 3.8 12.3 - - - +
266G ILE* 3.9 5.4 - - - +
267G ILE* 1.3 69.9 - - - +
269G LYS* 1.3 62.6 + - - +
270G ILE* 3.6 1.7 + - - +
282G ILE* 3.9 8.5 - - - -
286G SER* 2.6 29.5 + - - -
288G GLY 3.1 7.7 + - - -
289G ILE* 3.5 20.0 - - - +
290G MET 2.8 22.2 + - - +
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Residues in contact with LYS 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 3.6 0.4 - - - +
112G ASP* 3.2 31.1 + - - +
240G PHE* 3.7 18.2 - - + +
241G ALA 3.1 12.7 + - - +
242G SER* 2.9 28.5 + - - +
244G ILE* 3.4 27.7 + - - +
267G ILE 3.5 0.2 + - - -
268G SER* 1.3 71.2 - - - +
270G ILE* 1.3 61.9 + - - +
271G GLU* 3.4 26.9 + - + +
290G MET* 3.5 46.0 - - + +
292G ALA* 4.4 1.6 - - + -
532G K 3.5 3.8 - - - -
533G MG 3.9 0.6 - - - -
534G PYR 3.0 23.8 + - - -
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Residues in contact with ILE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G ILE 4.3 6.1 - - - +
268G SER* 4.0 1.8 - - - +
269G LYS* 1.3 77.2 - - - +
271G GLU* 1.3 60.9 + - - +
272G ASN 4.4 0.9 - - - +
275G GLY* 3.7 25.4 - - - +
276G VAL* 3.7 30.3 - - + +
279G PHE* 4.3 4.5 - - + -
282G ILE* 3.9 32.8 - - + -
289G ILE* 3.8 31.2 - - + -
290G MET 2.9 8.9 + - - +
291G VAL 4.5 0.3 - - - -
292G ALA* 3.6 15.8 + - - +
296G LEU* 3.5 14.0 - - - +
312G MET* 3.8 19.5 - - + -
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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