Contacts of the strand formed by residues 187 - 196 (chain A) in PDB entry 4I7C
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 PHE 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLN 4.0 0.3 - - - +
183A SER* 3.5 4.9 + - - -
184A CYS 2.9 31.1 + - - +
185A PHE 3.2 24.7 - - - -
186A GLY* 1.3 83.2 - - - +
188A HIS* 1.3 66.2 + - - +
189A PHE* 3.9 6.7 - - + -
211A LEU* 3.7 29.6 - - + -
212A ILE 4.3 9.2 - - - -
213A GLY* 5.2 0.2 - - - -
217A GLN* 3.7 42.8 - - + -
221A PHE* 3.6 24.2 - + - -
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Residues in contact with HIS 188 (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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145A MET* 3.5 51.0 - - + +
157A THR* 4.2 13.9 - - + +
159A GLN* 4.7 4.9 - - - -
181A MET* 4.9 4.3 - - + +
182A GLN 3.6 2.7 + - - +
183A SER* 3.7 28.3 + - - -
186A GLY 4.7 4.6 + - - -
187A PHE* 1.3 82.4 - - - +
189A PHE* 1.3 62.6 + - - +
211A LEU* 3.5 5.4 - - - +
212A ILE* 2.9 37.3 + - + +
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Residues in contact with PHE 189 (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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181A MET* 2.8 16.3 - - - +
182A GLN 2.8 36.9 + - - +
184A CYS* 3.8 32.8 - - - -
187A PHE* 3.9 8.5 - - + -
188A HIS* 1.3 76.1 - - - +
190A MET* 1.3 59.7 + - - +
191A LEU* 4.0 4.3 - - + -
209A VAL* 4.1 16.8 - - + -
210A GLN 3.4 4.7 - - - +
211A LEU* 3.6 35.4 - - + -
221A PHE* 3.9 30.5 - + - -
240A PRO* 4.3 9.0 - - + -
279A ILE* 3.4 43.3 - - + -
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Residues in contact with MET 190 (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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129A PRO* 3.5 39.9 - - + +
130A CYS 4.6 0.2 - - - +
131A PRO* 4.5 4.0 - - - -
148A LEU* 4.0 25.1 - - + -
155A ILE* 4.6 5.8 - - + -
179A VAL* 3.7 29.2 - - + -
180A MET 4.2 0.2 - - - +
181A MET* 3.2 22.4 - - + +
188A HIS 4.5 0.2 + - - -
189A PHE* 1.3 71.5 - - - +
191A LEU* 1.3 64.4 + - - +
192A VAL* 3.8 11.6 + - + +
208A ILE 3.9 0.9 - - - +
209A VAL* 3.4 4.2 - - - -
210A GLN* 2.7 60.9 + - + +
212A ILE* 4.6 6.0 - - + +
243A ILE* 5.4 0.2 - - + -
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Residues in contact with LEU 191 (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 ILE* 3.7 17.0 - - + -
165A PHE* 4.0 18.1 - - + -
178A TRP 3.8 0.3 - - - +
179A VAL* 3.5 6.6 - - - +
180A MET* 2.8 43.5 + - + +
182A GLN* 3.3 41.3 - - + +
189A PHE* 4.0 6.5 - - + +
190A MET* 1.3 77.4 - - - +
192A VAL* 1.3 62.0 + - - +
208A ILE 3.9 4.5 - - - -
209A VAL* 4.0 22.2 - - + -
225A LEU* 5.8 0.2 - - + -
277A VAL* 3.7 28.5 - - + -
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Residues in contact with VAL 192 (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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131A PRO* 4.0 24.5 - - + -
165A PHE* 4.3 4.8 - - - -
177A ASP* 4.7 3.4 - - - +
178A TRP 3.6 5.4 - - - +
179A VAL* 4.6 2.2 - - + -
190A MET* 3.8 28.7 - - + +
191A LEU* 1.3 79.1 - - - +
193A LEU* 1.3 73.4 + - - +
194A GLU* 4.7 7.2 - - + +
206A PHE 3.7 1.1 - - - +
207A ALA* 3.3 5.5 - - - +
208A ILE* 3.0 40.6 + - + +
210A GLN* 4.2 3.4 - - + +
247A ILE* 3.9 29.6 - - + -
251A ILE* 5.5 1.1 - - + -
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Residues in contact with LEU 193 (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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165A PHE* 4.1 10.0 - - + -
167A ALA* 3.5 26.0 - - + -
170A ILE* 4.9 5.2 - - + -
177A ASP* 3.5 6.4 - - - +
178A TRP* 3.0 69.7 + - + +
192A VAL* 1.3 74.8 - - - +
194A GLU* 1.3 62.7 + - - +
205A PHE* 4.1 17.3 - - + -
206A PHE 3.3 13.7 - - - +
207A ALA* 4.1 8.5 - - + -
259A PHE* 4.1 19.5 - - + -
273A LEU* 5.3 0.4 - - + -
275A ILE* 4.0 22.9 - - + -
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Residues in contact with GLU 194 (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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131A PRO* 5.9 0.3 - - - +
176A VAL 3.5 5.6 - - - +
177A ASP* 3.9 6.1 - - - +
192A VAL* 4.9 4.6 - - + +
193A LEU* 1.3 76.3 - - - +
195A LYS* 1.3 66.7 + - - +
196A GLN* 2.6 34.4 + - - +
205A PHE* 3.4 4.9 - - - -
206A PHE* 2.8 48.0 + - + +
247A ILE* 5.6 0.7 - - - +
251A ILE* 3.3 25.0 - - + +
125B ARG* 3.4 35.2 + - - +
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Residues in contact with LYS 195 (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 ILE 3.0 19.7 + - - +
171A ASN* 3.5 13.1 + - - +
172A LEU 2.9 28.0 + - - +
174A GLY 3.8 8.1 - - - +
175A ALA* 3.3 7.1 - - - +
176A VAL* 3.0 35.0 + - + +
178A TRP* 3.9 16.9 - - + -
194A GLU* 1.3 74.7 - - - +
196A GLN* 1.3 61.6 + - - +
203A GLN* 3.3 38.2 - - + +
204A GLN 3.5 7.6 - - - +
205A PHE* 3.6 34.7 - - + -
261A THR* 3.9 13.0 - - - +
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Residues in contact with GLN 196 (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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174A GLY 4.6 1.3 - - - -
175A ALA* 4.8 3.4 - - + +
194A GLU* 2.6 34.3 + - - +
195A LYS* 1.3 73.9 - - - +
197A GLU* 1.3 66.5 + - - +
203A GLN* 3.1 28.2 - - - +
204A GLN* 2.9 19.6 + - + +
206A PHE* 3.3 27.7 - - + -
251A ILE* 3.9 16.7 - - - +
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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