Contacts of the strand formed by residues 185 - 197 (chain A) in PDB entry 6YB9
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 CYS 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLU 5.0 0.7 - - - +
180A TRP* 3.4 42.1 + - + +
181A LEU* 3.9 11.3 + - - +
183A GLN* 3.2 14.5 - - - -
184A ASN* 1.3 78.6 - - - +
186A THR* 1.3 61.7 + - - +
187A LEU 3.7 2.6 + - - -
216A LEU* 3.8 22.9 - - + -
217A TRP 3.7 5.8 - - - +
218A PRO* 4.4 8.1 - - + -
251A TRP* 3.6 36.1 - - - -
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Residues in contact with THR 186 (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 ARG* 6.0 1.6 - - + -
103A ILE* 3.7 30.3 - - + -
120A LYS* 5.5 2.7 - - - +
177A GLU* 6.1 0.4 - - - +
181A LEU* 5.7 4.6 - - - +
184A ASN 4.3 0.2 - - - -
185A CYS* 1.3 70.9 - - - +
187A LEU* 1.3 70.4 + - - +
188A VAL* 3.4 7.3 + - + +
215A ARG 3.8 0.3 - - - +
216A LEU* 3.6 4.5 - - - -
217A TRP* 2.9 38.0 + - + -
219A SER 4.4 0.3 - - - -
220A GLY* 3.3 26.4 + - - -
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Residues in contact with LEU 187 (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 ARG* 4.0 6.9 - - - +
173A PHE* 3.6 39.3 - - + +
176A LEU* 3.6 17.7 - - + +
177A GLU* 3.5 47.3 + - - +
180A TRP* 4.3 10.5 - - + +
185A CYS 3.7 4.6 + - - -
186A THR* 1.3 73.4 - - - +
188A VAL* 1.3 61.1 + - - +
189A ASP 4.1 2.2 - - - +
190A MET* 4.9 5.2 - - - -
214A TRP* 3.6 43.7 - - + -
215A ARG 3.6 7.9 - - - +
216A LEU* 4.2 10.5 - - + +
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Residues in contact with VAL 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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102A ARG* 2.9 26.7 + - - -
103A ILE* 3.3 31.3 + - + +
105A THR* 3.7 29.4 - - + -
173A PHE* 4.1 1.1 - - - -
186A THR* 3.8 14.4 - - + +
187A LEU* 1.3 72.3 - - - +
189A ASP* 1.3 67.3 + - - +
215A ARG* 3.0 16.5 + - + +
217A TRP* 3.4 49.1 - - + +
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Residues in contact with ASP 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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99A VAL* 4.9 0.2 - - + -
100A CYS 3.1 17.3 - - - +
101A ARG* 3.7 21.8 + - + -
103A ILE 4.6 1.6 - - - +
105A THR* 3.6 13.3 - - - +
173A PHE* 3.8 6.5 - - - -
187A LEU* 3.7 3.5 - - - +
188A VAL* 1.3 82.3 - - + +
190A MET* 1.3 64.7 + - - +
214A TRP* 3.3 4.3 - - - +
215A ARG* 2.8 52.6 + - - +
502A OK8 2.7 31.8 + - - -
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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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98A TRP 3.9 0.4 - - - +
99A VAL* 3.2 7.8 - - - +
100A CYS* 3.0 32.7 + - + +
169A THR* 3.7 10.8 - - + +
172A ILE* 3.7 13.5 - - + -
173A PHE* 3.4 55.2 - - + +
176A LEU* 4.0 23.3 - - - -
187A LEU* 4.9 3.6 - - + -
189A ASP* 1.3 78.3 + - - +
191A LYS* 1.3 61.9 - - - +
192A ILE* 3.8 24.9 - - + -
209A ILE* 5.2 2.5 - - + -
213A SER* 3.1 14.1 - - - +
214A TRP* 4.0 10.1 - - + -
502A OK8 3.8 7.0 - - - -
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Residues in contact with LYS 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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97A GLU* 3.7 35.2 + - + -
98A TRP 3.2 8.7 - - - +
99A VAL* 4.2 4.3 - - + -
131A LYS* 5.1 0.2 - - - +
190A MET* 1.3 71.7 - - - +
192A ILE* 1.3 81.5 + - - +
193A GLU* 3.0 26.1 + - - +
207A ASP* 4.4 9.7 + - - -
208A VAL 5.0 2.7 + - - +
209A ILE* 5.0 0.7 - - - +
213A SER* 2.7 36.0 + - - +
502A OK8 3.4 60.9 + - + +
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Residues in contact with ILE 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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98A TRP* 3.0 45.9 + - + +
169A THR* 3.8 17.9 - - + +
172A ILE* 3.8 20.4 - - + -
190A MET* 3.8 24.0 - - + -
191A LYS* 1.3 81.4 - - - +
193A GLU* 1.3 68.6 + - - +
194A PHE* 3.6 30.3 - - + -
205A LEU* 3.8 11.7 - - + -
208A VAL 5.2 5.4 - - - -
209A ILE* 3.9 26.7 - - + -
213A SER* 6.0 0.2 - - - -
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Residues in contact with GLU 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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93A MET* 3.9 24.9 - - + +
94A ILE 4.8 2.7 - - - +
96A ILE 3.9 15.7 - - - +
97A GLU* 3.8 3.9 - - + +
131A LYS* 2.9 42.9 + - - +
191A LYS* 3.0 28.4 + - + +
192A ILE* 1.3 79.9 - - - +
194A PHE* 1.3 65.6 + - - +
205A LEU* 3.7 6.4 - - - +
206A ALA 3.1 28.3 + - - +
207A ASP* 4.3 20.0 - - + +
208A VAL 5.5 0.8 + - - -
501A ANP 4.2 8.8 + - - -
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Residues in contact with PHE 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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93A MET* 3.7 10.3 - - - +
94A ILE* 3.0 27.3 + - - +
96A ILE 4.9 1.2 + - - -
98A TRP* 3.5 17.0 - + - -
165A MET* 3.2 54.4 - - + +
168A ALA* 3.9 12.3 - - + -
169A THR* 3.4 17.3 - - - -
172A ILE* 4.3 5.4 - - + -
192A ILE* 3.6 24.9 - - + -
193A GLU* 1.3 72.8 - - - +
195A GLY* 1.3 58.7 + - - +
203A ILE* 3.9 15.3 - - + -
204A VAL 3.3 9.4 - - - +
205A LEU* 3.5 23.8 - - - -
504A EDO 3.9 21.3 - - - -
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Residues in contact with GLY 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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91A CYS* 4.0 7.9 - - - -
92A GLU 3.3 12.8 - - - -
93A MET* 4.0 12.6 - - - -
94A ILE* 4.1 5.2 - - - -
194A PHE* 1.3 73.5 - - - +
196A VAL* 1.3 63.1 + - - -
197A ASP 4.0 0.2 - - - -
202A GLU 3.8 0.3 - - - +
203A ILE* 3.4 3.1 - - - +
204A VAL* 2.9 35.3 + - - +
206A ALA* 4.1 4.0 - - - +
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Residues in contact with VAL 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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91A CYS* 3.1 2.9 - - - -
92A GLU* 2.9 36.3 + - - +
94A ILE* 4.1 14.6 - - + -
152A PHE* 3.7 39.7 - - + +
153A ALA* 3.9 8.4 - - + +
155A LEU* 4.1 23.6 - - + -
157A ILE* 4.6 2.5 - - + -
195A GLY* 1.3 73.8 - - - +
197A ASP* 1.3 67.8 + - - +
198A VAL* 3.3 2.1 + - - +
201A LYS* 3.8 33.0 - - + +
202A GLU 3.5 3.6 - - - +
203A ILE* 4.4 2.5 - - + -
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Residues in contact with ASP 197 (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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29A GLY 5.2 1.0 - - - +
89A PRO* 3.3 31.2 - - - +
90A GLN 3.6 8.1 - - - +
91A CYS* 4.0 9.0 - - - -
195A GLY 4.0 2.2 + - - -
196A VAL* 1.3 68.8 - - - +
198A VAL* 1.3 58.2 + - - +
199A THR* 2.7 36.4 + - - -
200A THR* 3.1 34.2 + - - +
201A LYS* 2.8 33.1 + - - +
202A GLU 3.1 14.3 + - - +
204A VAL* 4.6 10.8 - - + +
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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