Contacts of the strand formed by residues 265 - 276 (chain A) in PDB entry 5E5R
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A PHE* 5.7 0.4 - - + -
197A ILE* 3.5 23.3 - - + +
199A ALA* 3.8 20.4 - - + -
253A THR* 3.5 4.3 - - - +
254A GLY* 2.6 36.4 + - - -
255A SER* 3.5 25.1 - - - +
256A LEU* 3.6 17.7 - - + +
264A ILE* 1.3 86.8 - - + +
266A GLU* 1.3 63.0 + - - +
267A TRP* 3.3 34.8 - - + +
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Residues in contact with GLU 266 (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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138A GLY 5.8 0.2 - - - -
139A LEU* 4.0 15.9 - - + +
140A PRO* 4.8 6.5 - - + -
196A ILE* 4.2 24.3 - - + +
197A ILE 3.1 11.6 + - - +
198A GLY* 3.5 3.2 - - - -
199A ALA 3.0 22.9 + - - +
251A ARG* 3.1 36.4 + - - +
252A TYR 3.2 8.8 - - - +
253A THR* 2.8 25.8 + - - +
264A ILE 6.0 0.2 - - - -
265A VAL* 1.3 72.1 - - - +
267A TRP* 1.3 62.8 + - - +
268A ILE* 4.9 1.4 - - - +
278C TYR* 3.7 24.4 - - - -
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Residues in contact with TRP 267 (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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84A SER* 3.0 27.2 + - - -
163A HIS* 3.6 22.9 - + - -
175A GLN* 3.5 31.6 - - + -
177A PHE* 4.3 9.6 - + - -
199A ALA* 3.4 34.5 - - + -
200A MET 4.0 11.0 - - - -
201A ALA* 4.3 7.4 - - + -
250A TYR 4.5 0.2 - - - -
251A ARG* 2.9 32.6 + - - -
252A TYR* 3.0 37.8 + + + +
254A GLY* 3.9 4.0 - - - -
255A SER 3.2 21.0 + - - -
256A LEU* 5.1 0.7 - - - -
257A THR* 4.0 15.9 - - + -
265A VAL* 3.3 28.0 - - + +
266A GLU* 1.3 74.1 - - - +
268A ILE* 1.3 63.4 - - - +
269A VAL* 4.2 3.1 - - + -
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Residues in contact with ILE 268 (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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102A LEU* 4.5 17.5 - - + -
134A VAL* 4.8 1.6 - - + -
137A ALA* 4.9 1.3 - - + -
139A LEU* 4.2 26.0 - - + -
178A PHE* 6.1 0.7 - - + -
198A GLY* 6.5 0.2 - - - -
199A ALA 2.7 16.3 + - - +
200A MET* 3.4 22.9 - - + +
201A ALA 2.6 34.7 + - - +
249A TYR* 3.8 28.5 - - + -
250A TYR 3.5 2.2 - - - -
251A ARG* 3.5 15.9 - - - +
266A GLU 4.9 2.5 - - - +
267A TRP* 1.3 79.6 - - - +
269A VAL* 1.3 58.8 + - - +
270A PHE* 3.8 23.5 + - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.7 30.7 - - + -
163A HIS* 4.3 22.0 - - + +
201A ALA* 3.6 15.3 - - + +
203A PHE* 3.6 35.7 - - + -
249A TYR* 3.4 1.3 - - - -
250A TYR* 3.1 36.6 + - + +
252A TYR* 4.5 15.3 - - + -
267A TRP* 4.8 0.9 - - + -
268A ILE* 1.3 77.0 - - - +
270A PHE* 1.3 66.5 + - - +
271A ARG 3.2 2.3 + - - -
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Residues in contact with PHE 270 (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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102A LEU* 3.5 30.5 - - + -
200A MET* 3.7 31.4 - - + -
201A ALA 3.2 20.0 + - - +
202A ILE* 4.1 12.3 - - + -
203A PHE* 3.8 18.4 + - - -
242A LEU* 4.3 9.0 - - + -
243A PRO* 3.5 23.3 - - + -
245A SER 4.8 0.2 - - - -
246A LEU* 3.7 52.7 - - + -
248A SER 4.5 1.6 - - - +
249A TYR* 3.8 10.8 - - + -
268A ILE* 3.9 17.9 - - + -
269A VAL* 1.3 70.5 - - - +
271A ARG* 1.3 65.7 + - - +
272A ARG 3.5 4.6 + - - +
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Residues in contact with ARG 271 (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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90A ASP* 3.9 20.4 + - - -
170A PHE* 5.2 4.7 - - - -
203A PHE* 4.5 10.6 - - - -
248A SER* 2.9 40.2 + - - +
250A TYR* 3.4 31.8 + - + +
269A VAL* 3.2 5.0 + - - -
270A PHE* 1.3 73.0 - - - +
272A ARG* 1.3 103.4 + - - +
273A PRO* 3.9 4.3 - - - +
319A LYS* 4.4 12.5 - - - +
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Residues in contact with ARG 272 (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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203A PHE* 4.5 3.0 + - - +
243A PRO* 2.9 37.2 - - + +
244A ALA 5.6 0.4 - - - +
245A SER* 3.9 29.6 + - - +
248A SER* 4.2 13.5 + - - -
270A PHE* 3.4 7.4 - - - +
271A ARG* 1.3 134.7 + - + +
273A PRO* 1.3 72.5 - - + +
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Residues in contact with PRO 273 (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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170A PHE* 4.5 11.4 - - + -
203A PHE* 3.1 26.7 - - + +
204A PHE 4.3 0.2 - - - -
205A GLN* 3.8 31.9 - - + +
243A PRO* 4.5 6.6 - - - +
244A ALA 5.0 2.4 + - - -
271A ARG 4.0 4.3 - - - +
272A ARG* 1.3 94.2 - - + +
274A VAL* 1.3 63.9 + - - +
275A PRO* 4.0 6.1 - - - +
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Residues in contact with VAL 274 (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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202A ILE* 3.8 11.0 - - + -
203A PHE 2.7 8.7 + - - -
204A PHE* 3.2 25.4 - - + +
205A GLN* 2.9 21.2 + - - -
211A ASN* 3.5 22.4 - - - +
214A LEU* 4.4 8.1 - - + -
240A ASP 4.5 10.8 - - - +
241A LEU 3.8 12.8 - - - +
242A LEU 3.5 33.9 - - - +
243A PRO* 3.7 5.8 - - + -
273A PRO* 1.3 72.7 - - - +
275A PRO* 1.3 73.8 - - + +
276A ILE 3.6 0.2 + - - -
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Residues in contact with PRO 275 (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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205A GLN* 3.3 7.9 - - + +
206A VAL 5.1 0.2 - - - +
207A SER* 3.7 23.1 - - - +
209A ARG 5.3 0.4 - - - +
211A ASN* 2.9 44.2 + - + +
244A ALA 6.3 0.7 - - - +
273A PRO 4.0 6.1 - - - +
274A VAL* 1.3 91.7 - - + +
276A ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 276 (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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171A PRO* 4.1 8.3 - - + -
172A VAL* 5.3 2.0 - - + -
204A PHE* 3.7 28.0 - - + -
205A GLN 2.9 22.1 + - - +
206A VAL* 3.2 12.4 - - - +
207A SER* 2.6 35.7 + - - -
211A ASN* 4.7 0.9 - - - -
214A LEU* 3.3 33.2 - - + -
218A ILE* 5.4 3.6 - - + -
275A PRO* 1.3 68.0 - - - +
277A SER* 1.3 59.8 + - - +
280A GLN* 3.8 18.2 - - + +
281A LEU* 3.7 34.5 - - + +
284A PHE* 5.8 4.5 - - + -
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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