Contacts of the strand formed by residues 197 - 206 (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 ILE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A PHE* 4.2 3.6 - - - -
177A PHE* 4.8 9.9 - - + -
178A PHE 3.1 19.7 - - - +
179A TYR* 4.4 2.7 - - + -
187A PHE* 4.0 22.4 - - + -
190A ALA* 4.2 12.6 - - + -
191A ILE* 3.9 24.9 - - + -
195A ARG 3.5 6.3 + - - +
196A ILE* 1.3 85.8 - - - +
198A GLY* 1.3 57.8 + - - +
256A LEU* 4.1 26.0 - - + -
264A ILE* 3.0 17.5 + - + +
265A VAL* 3.5 13.5 - - + -
266A GLU* 3.1 24.1 + - - -
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Residues in contact with GLY 198 (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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139A LEU* 5.2 8.3 - - - -
143A PHE* 3.9 14.3 - - - -
177A PHE* 3.5 3.3 - - - +
178A PHE* 2.8 43.3 + - - +
197A ILE* 1.3 78.6 - - - +
199A ALA* 1.3 63.6 + - - +
265A VAL* 4.6 0.7 - - - -
266A GLU* 3.5 9.4 - - - -
268A ILE* 6.5 0.4 - - - -
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Residues in contact with ALA 199 (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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176A ILE 3.2 5.8 - - - +
177A PHE* 3.8 22.9 - - + -
178A PHE* 4.3 1.1 - - - -
198A GLY* 1.3 74.6 - - - +
200A MET* 1.3 58.4 + - - +
265A VAL* 3.8 13.4 - - + +
266A GLU 3.0 8.3 + - - +
267A TRP* 3.4 29.4 - - + -
268A ILE* 2.7 36.5 + - - +
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Residues in contact with MET 200 (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* 4.6 0.9 - - + -
104A LEU* 3.9 17.5 - - + -
107A PHE* 4.4 3.4 - - + -
134A VAL* 3.6 31.6 - - + -
175A GLN* 3.1 27.9 - - - +
176A ILE* 2.9 20.6 + - + +
178A PHE* 3.7 27.1 - - + -
199A ALA* 1.3 76.3 - - - +
201A ALA* 1.3 60.9 + - - +
202A ILE* 3.6 14.4 - - + -
242A LEU* 4.3 17.9 - - + -
267A TRP* 4.0 2.9 - - - -
268A ILE* 3.4 17.7 - - + +
270A PHE* 3.7 30.5 - - + -
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Residues in contact with ALA 201 (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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163A HIS* 3.6 18.8 - - + +
173A GLU* 3.4 26.7 - - - +
174A MET 3.3 4.3 - - - -
175A GLN* 4.8 0.2 - - + -
200A MET* 1.3 74.4 - - - +
202A ILE* 1.3 65.4 + - - +
203A PHE* 4.2 1.0 + - - -
267A TRP* 4.3 4.9 - - + -
268A ILE 2.6 14.7 + - - +
269A VAL* 3.6 13.8 - - + +
270A PHE* 3.2 25.1 + - - +
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Residues in contact with ILE 202 (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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173A GLU* 3.6 1.3 - - - +
174A MET* 2.7 68.5 + - + +
176A ILE* 4.0 4.7 - - + -
200A MET* 3.6 25.8 - - + +
201A ALA* 1.3 79.6 - - - +
203A PHE* 1.3 65.6 + - - +
204A PHE* 3.8 7.1 + - + -
241A LEU 3.5 19.1 - - - +
242A LEU* 3.6 23.1 - - + -
243A PRO* 4.0 13.0 - - + -
270A PHE* 4.1 13.0 - - + -
274A VAL* 3.8 20.0 - - + -
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Residues in contact with PHE 203 (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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88A ILE* 5.6 1.3 - - + -
161A SER* 3.8 12.8 - - - -
163A HIS* 3.6 38.1 - - + -
164A SER* 4.0 7.4 - - - -
170A PHE* 3.4 42.6 - + + -
172A VAL 3.8 1.1 - - - -
173A GLU* 3.3 30.1 - - + -
201A ALA* 5.6 0.2 - - + -
202A ILE* 1.3 74.8 - - - +
204A PHE* 1.3 58.6 + - - +
269A VAL* 3.6 21.8 - - + -
270A PHE 3.8 19.6 + - - +
271A ARG* 4.5 7.6 - - - -
272A ARG 4.8 1.4 + - - -
273A PRO* 3.1 15.7 - - + +
274A VAL* 2.7 30.2 + - - +
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Residues in contact with PHE 204 (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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150A PHE* 4.5 11.4 - + - -
170A PHE* 3.2 21.3 - - - +
171A PRO* 3.3 10.0 - - - +
172A VAL* 2.9 41.1 + - + +
174A MET* 4.1 24.2 - - + -
202A ILE* 3.9 21.8 - - + -
203A PHE* 1.3 81.8 - - - +
205A GLN* 1.3 59.9 + - - +
214A LEU* 4.1 28.7 - - + -
217A ILE* 6.2 1.3 - - + -
241A LEU 4.0 6.7 - - - -
274A VAL* 3.2 28.9 - - + +
276A ILE* 3.7 26.2 - - + -
284A PHE* 5.3 6.3 - + - -
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Residues in contact with GLN 205 (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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168A ARG* 3.3 37.3 + - - +
169A ARG 5.0 1.3 + - - +
170A PHE* 3.3 26.5 - - + -
171A PRO* 3.6 13.2 - - - +
204A PHE* 1.3 74.4 - - - +
206A VAL* 1.3 100.3 + - + +
273A PRO* 3.8 26.0 - - + +
274A VAL 2.9 6.8 + - - +
275A PRO* 3.3 6.2 - - + +
276A ILE* 2.9 24.1 + - - -
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Residues in contact with VAL 206 (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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157A GLY* 4.5 4.0 - - - -
171A PRO* 4.1 9.3 - - + +
205A GLN* 1.3 100.6 + - + +
207A SER* 1.3 61.7 + - - +
275A PRO* 5.1 0.3 - - - +
276A ILE* 3.2 9.1 - - + +
278A TYR* 3.5 42.6 - - + +
281A LEU* 3.8 22.7 - - + -
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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