Contacts of the strand formed by residues 264 - 271 (chain L) in PDB entry 3Q3G
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 264 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219L VAL* 3.9 19.3 - - + -
223L PHE* 3.6 40.8 - - + -
235L LYS* 3.5 6.3 - - + +
237L LEU* 3.8 28.5 - - + -
259L ALA* 2.8 28.0 + - + +
260L ASP* 4.4 1.4 + - - +
262L GLU* 4.3 13.2 - - + +
263L GLY* 1.3 73.3 - - - +
265L ILE* 1.3 64.7 + - - +
266L ARG* 3.0 31.6 + - + +
289L SER* 3.7 1.6 + - - -
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Residues in contact with ILE 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L PHE* 4.1 24.0 - - + -
235L LYS 2.7 26.9 + - - +
236L ILE* 3.3 19.4 - - + +
237L LEU* 2.7 27.2 + - - +
263L GLY 4.4 6.1 - - - +
264L VAL* 1.3 69.5 - - - +
266L ARG* 1.3 61.9 + - - +
267L TYR* 3.7 25.6 - - + +
289L SER* 3.7 6.1 - - - +
295L HIS* 3.9 19.1 - - - +
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Residues in contact with ARG 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L ILE* 5.1 4.3 - - - -
237L LEU* 3.3 28.0 - - + +
239L VAL* 4.6 5.6 - - + -
256L ILE* 3.2 36.7 - - - +
259L ALA* 3.9 24.8 - - - +
260L ASP* 2.8 34.9 + - - +
264L VAL* 3.0 27.0 + - + -
265L ILE* 1.3 74.5 - - - +
267L TYR* 1.3 62.8 + - - +
286L THR 4.8 0.2 + - - -
287L ILE* 3.0 29.6 + - + +
288L ALA* 3.4 10.2 + - - -
289L SER* 2.9 51.6 + - - +
290L LYS* 6.1 2.0 - - - +
295L HIS* 3.4 9.6 - - - +
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Residues in contact with TYR 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236L ILE* 3.8 22.2 - - + -
237L LEU 2.7 11.6 + - - +
238L VAL* 4.0 14.8 - - + -
239L VAL* 2.7 35.3 + - - +
265L ILE* 3.7 21.4 - - + +
266L ARG* 1.3 74.8 - - - +
268L VAL* 1.3 55.2 + - - +
269L ILE* 5.7 0.9 - - + -
288L ALA* 5.1 0.2 - - - -
294L ASP 3.3 21.9 + - - -
295L HIS* 3.4 29.1 + + - -
297L PHE* 4.1 14.4 - + + -
312L LEU* 4.2 10.3 - - + -
315L LYS* 3.1 39.9 + - + +
316L ILE* 3.7 19.1 - - + -
318L ALA 4.7 1.9 + - - -
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Residues in contact with VAL 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L VAL* 3.3 16.2 - - + +
241L THR* 4.2 10.5 - - + -
267L TYR* 1.3 73.7 - - - +
269L ILE* 1.3 59.2 + - - +
284L LEU* 3.2 56.3 - - + +
287L ILE* 3.8 27.8 - - + -
288L ALA* 3.7 11.2 - - + +
295L HIS 3.0 8.7 + - - +
296L VAL* 4.0 8.5 - - + -
297L PHE* 2.8 34.8 + - - +
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Residues in contact with ILE 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L PHE* 3.7 31.9 - - + -
238L VAL* 3.9 13.7 - - + -
239L VAL 2.8 12.0 + - - +
240L ILE* 3.5 24.0 - - + -
241L THR 3.0 28.5 + - - +
267L TYR* 5.7 0.7 - - + -
268L VAL* 1.3 76.6 - - - +
270L GLY* 1.3 58.6 + - - +
271L VAL* 3.6 11.6 + - + +
297L PHE* 3.6 17.0 - - + +
299L VAL* 4.1 7.0 - - + -
305L LEU* 3.4 25.4 - - + -
308L ILE* 3.8 19.1 - - + -
312L LEU* 4.7 6.5 - - + -
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Residues in contact with GLY 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241L THR 3.4 7.2 - - - -
268L VAL 4.0 0.6 - - - -
269L ILE* 1.3 70.8 - - - +
271L VAL* 1.3 61.0 + - - -
272L GLY 4.0 1.0 + - - +
275L PHE* 3.6 21.8 - - - +
284L LEU* 3.8 18.3 - - - +
297L PHE 3.2 10.7 + - - -
298L GLN* 3.5 8.7 + - - +
299L VAL 3.2 23.6 + - - +
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Residues in contact with VAL 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240L ILE* 3.9 21.5 - - + -
241L THR 2.9 11.7 + - - +
242L ASP* 3.4 28.2 - - - +
269L ILE* 3.8 15.7 - - + +
270L GLY* 1.3 73.9 - - - -
272L GLY* 1.3 64.3 - - - +
275L PHE* 3.8 1.7 - - - -
299L VAL* 3.6 17.0 - - + -
301L ASN* 3.5 33.9 - - - +
302L PHE* 3.5 36.0 - - + +
305L LEU* 4.4 3.4 - - + -
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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