Contacts of the strand formed by residues 252 - 262 (chain E) in PDB entry 6GL7
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 GLU 252 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E LEU 5.6 0.3 - - - +
161E LYS* 5.4 6.9 + - - +
162E PRO* 3.3 35.6 - - + +
243E CYS 3.9 0.7 - - - +
244E THR* 3.4 4.0 - - - -
245E VAL* 3.1 44.9 + - + +
246E HIS* 5.1 4.0 + - - -
250E ARG 3.8 9.1 - - - +
251E GLU* 1.3 80.4 - - - +
253E VAL* 1.3 63.6 + - - +
254E VAL 4.2 0.7 + - - -
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Residues in contact with VAL 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E PRO* 5.5 0.6 - - - +
205E ARG* 5.6 4.5 - - - +
242E VAL* 3.5 27.6 - - + -
243E CYS 3.4 5.4 - - - +
244E THR* 3.6 23.8 - - + +
251E GLU* 5.6 2.5 - - + -
252E GLU* 1.3 77.9 - - - +
254E VAL* 1.3 65.1 + - - +
255E MET* 4.8 9.2 - - + -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E PRO* 3.7 33.7 - - + +
163E ARG* 4.2 24.0 - - + +
167E PHE* 3.5 8.7 - - + -
242E VAL* 3.5 2.5 - - - +
243E CYS* 3.0 52.0 + - - +
253E VAL* 1.3 75.4 - - - +
255E MET* 1.3 72.6 + - - +
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Residues in contact with MET 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E PHE* 4.1 1.3 - - - -
207E LEU* 4.4 12.6 - - + -
240E VAL* 3.7 22.4 - - + -
241E ALA 3.0 15.9 - - - +
242E VAL* 3.9 21.1 - - + -
253E VAL* 4.8 8.5 - - + -
254E VAL* 1.3 80.1 - - - +
256E VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E ARG* 3.8 33.4 - - - +
167E PHE* 3.5 47.6 - - + -
171E ARG* 5.9 1.1 - - + -
172E PRO* 4.9 11.9 - - + -
240E VAL* 3.8 5.2 - - - +
241E ALA* 2.8 36.0 + - + +
254E VAL* 5.1 0.4 - - + -
255E MET* 1.3 80.4 - - - +
257E PRO* 1.3 82.7 - - + +
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Residues in contact with PRO 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ARG* 4.0 41.5 - - + +
172E PRO* 4.1 10.9 - - - +
238E GLU* 4.1 20.0 - - - +
239E LEU 3.7 5.2 - - - +
240E VAL* 4.9 2.0 - - + -
256E VAL* 1.3 101.1 - - + +
258E PHE* 1.3 57.9 + - - +
259E PRO* 3.3 17.7 - - + +
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E PRO* 5.0 4.9 - - + -
174E PHE* 3.1 39.3 - + - -
185E PHE* 3.6 28.3 - + - -
188E PHE* 3.4 37.9 - + - -
206E LEU* 4.3 9.2 - - + -
214E PHE* 4.2 9.6 - + - -
223E VAL* 4.2 4.5 - - + -
237E TYR 4.4 0.2 - - - -
238E GLU* 3.6 2.3 - - - +
239E LEU* 2.7 54.8 + - + +
240E VAL 4.5 0.2 - - - -
241E ALA* 3.9 13.9 - - + +
257E PRO* 1.3 74.0 - - - +
259E PRO* 1.3 63.4 - - - +
260E VAL* 3.8 15.5 + - + +
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Residues in contact with PRO 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E ARG* 5.9 2.5 - - + -
172E PRO* 3.4 22.0 - - + +
173E SER* 3.9 6.5 - - - +
174E PHE* 3.2 28.3 + - - -
237E TYR 3.4 9.9 - - - +
238E GLU* 4.1 13.7 - - + -
257E PRO* 3.3 18.4 - - + +
258E PHE* 1.3 89.4 - - - +
260E VAL* 1.3 59.8 + - - +
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Residues in contact with VAL 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E PHE* 3.6 32.5 - - + +
176E ILE* 3.5 33.9 - - + -
214E PHE* 3.8 29.8 - - + -
236E LYS* 3.9 4.5 - - - +
237E TYR* 2.9 41.1 + - + +
258E PHE* 3.9 14.1 - - + +
259E PRO* 1.3 80.9 - - - +
261E THR* 1.3 64.1 + - - +
262E VAL* 3.6 1.9 + - - +
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Residues in contact with THR 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLY 5.8 1.8 - - - +
330D ASN 4.8 7.4 - - - +
332D GLU* 6.2 2.0 - - + +
333D GLU* 3.0 38.4 + - + +
173E SER* 4.2 2.8 + - - -
174E PHE 2.6 18.2 + - - -
175E ARG* 3.5 3.3 - - - +
176E ILE* 2.8 31.4 + - - +
236E LYS* 5.6 1.3 - - - +
260E VAL* 1.3 70.1 - - - +
262E VAL* 1.3 66.3 + - - +
263E TYR* 3.6 27.7 - - + +
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Residues in contact with VAL 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLY 5.2 5.5 - - - +
330D ASN* 4.8 1.7 - - - +
176E ILE* 3.5 10.5 - - + -
178E GLU* 3.5 14.8 - - - +
229E LEU* 3.7 13.2 - - + -
234E ARG 3.9 10.5 - - - +
235E GLU* 3.3 21.5 + - - +
236E LYS* 3.6 15.6 - - - +
237E TYR* 3.5 38.1 - - + -
260E VAL 3.6 1.5 + - - +
261E THR* 1.3 82.8 - - - +
263E TYR* 1.3 75.8 + - - +
264E ASP* 5.5 1.0 - - - +
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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