Contacts of the strand formed by residues 191 - 200 (chain A) in PDB entry 3OF6
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 TYR 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR* 6.1 0.9 - - - +
152A GLY 3.2 15.2 + - - -
153A PHE* 3.0 51.9 + - + +
154A TYR* 3.8 24.2 - + - -
155A PRO* 3.8 2.2 - - + -
156A ASP* 3.5 50.5 + - + -
179A PRO* 3.8 22.2 - - + -
180A LEU 3.5 2.2 - - - -
181A LYS* 3.5 43.8 - - + -
182A GLU* 3.7 3.5 - - - +
189A SER 4.0 4.7 - - - -
190A ARG* 1.3 76.1 - - - +
192A CYS* 1.3 61.7 + - - +
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Residues in contact with CYS 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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150A ALA 3.2 9.0 - - - +
151A THR* 4.3 7.4 - - + -
153A PHE* 3.7 1.6 - - - -
179A PRO* 3.1 10.9 - - - +
180A LEU* 2.8 35.5 + - + +
182A GLU* 4.3 6.5 - - + -
191A TYR* 1.3 74.4 - - - +
193A LEU* 1.3 63.8 + - - +
58D PHE* 3.9 17.0 - - + -
60D TYR* 3.6 24.2 - - + +
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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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148A CYS 3.7 0.2 - - - +
149A LEU* 3.4 4.9 - - - -
150A ALA* 2.8 44.9 + - + +
153A PHE* 4.2 5.2 - - + -
158A VAL* 3.8 26.9 - - + +
160A LEU* 4.1 32.3 - - + +
175A THR* 4.1 8.5 - - + -
176A ASP* 3.6 29.8 - - + +
178A GLN 4.7 0.4 - - - +
179A PRO* 4.5 15.7 - - + -
192A CYS* 1.3 81.3 - - - +
194A SER* 1.3 72.4 + - - +
215A VAL* 5.5 0.4 - - + -
60D TYR* 3.7 9.9 - - - -
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Residues in contact with SER 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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148A CYS 3.2 5.6 - - - -
149A LEU* 3.6 19.3 - - - -
160A LEU* 4.6 0.9 - - - -
175A THR* 3.2 6.8 - - - +
176A ASP* 2.7 53.8 + - - +
193A LEU* 1.3 80.3 - - - +
195A SER* 1.3 62.5 + - - +
196A ARG* 3.6 7.2 + - - -
60D TYR* 3.6 14.6 - - - +
73D LEU* 3.8 15.6 - - - +
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Residues in contact with SER 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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147A VAL* 3.5 6.6 - - - +
148A CYS* 3.1 25.1 + - - -
160A LEU* 3.6 21.6 - - - +
162A TRP* 2.8 34.2 + - - -
173A VAL* 4.2 0.7 - - - +
174A SER 3.5 7.5 + - - -
175A THR* 2.8 23.9 + - - -
194A SER* 1.3 75.6 - - - +
196A ARG* 1.3 74.6 + - - +
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Residues in contact with ARG 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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145A THR* 4.0 19.3 - - + -
146A LEU 3.3 4.5 - - - +
147A VAL* 4.6 9.4 - - + -
162A TRP* 4.3 2.9 - - - -
172A GLY 3.0 6.6 - - - +
173A VAL* 3.5 1.0 - - - -
174A SER* 2.8 77.3 + - - +
175A THR 3.9 4.2 + - - -
176A ASP* 3.4 19.8 + - - -
194A SER* 3.6 13.9 + - - -
195A SER* 1.3 86.5 + - - +
197A LEU* 1.3 60.6 + - - +
198A ARG* 4.0 0.9 - - + -
32D LEU* 4.2 16.2 - - + -
34D LEU* 6.1 0.2 - - - -
63D SER* 3.2 31.5 + - - -
64D PRO 5.5 0.8 + - - -
65D ALA* 5.8 0.6 - - - +
71D THR* 3.3 26.9 + - - -
73D LEU* 4.9 9.3 - - + +
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Residues in contact with LEU 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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144A ALA 3.6 1.9 - - - +
145A THR* 3.3 3.3 - - - -
146A LEU* 2.9 42.6 + - + +
162A TRP* 3.8 46.0 - - + +
164A VAL* 3.8 26.2 - - + -
169A VAL* 4.0 5.8 - - + -
171A SER 3.7 22.9 - - - +
172A GLY 3.6 0.9 - - - +
173A VAL* 3.7 15.3 - - + +
196A ARG* 1.3 71.6 - - - +
198A ARG* 1.3 61.9 + - - +
199A VAL* 3.8 18.1 + - + -
211A PHE* 4.5 12.3 - - + -
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Residues in contact with ARG 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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137A GLU* 3.1 13.5 + - - -
141A THR* 3.3 23.2 + - - +
143A LYS* 3.3 45.8 + - + +
144A ALA 3.3 5.6 - - - +
145A THR* 3.0 29.6 + - + +
171A SER 5.1 0.3 - - - +
172A GLY* 3.1 28.4 + - - +
196A ARG 4.0 0.9 + - - +
197A LEU* 1.3 73.0 - - - +
199A VAL* 1.3 68.7 + - - +
34D LEU* 4.3 12.7 - - - +
67D ASP* 5.0 13.2 + - - -
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Residues in contact with VAL 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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143A LYS* 3.6 10.8 - - - +
144A ALA* 2.7 42.5 + - + +
146A LEU* 4.6 10.1 - - + -
164A VAL* 5.6 2.2 - - + -
197A LEU* 3.8 25.3 + - + -
198A ARG* 1.3 79.4 - - - +
200A SER* 1.3 66.1 + - - +
203A PHE* 4.2 23.3 - - + -
204A TRP* 4.1 21.8 - - + +
211A PHE* 4.6 6.5 - - + -
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Residues in contact with SER 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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142A GLN 4.2 5.6 - - - -
143A LYS* 4.3 12.7 - - - +
144A ALA 4.1 0.7 - - - -
199A VAL* 1.3 80.3 - - - +
201A ALA* 1.3 59.7 + - - +
202A THR* 3.2 18.6 + - - -
203A PHE* 2.8 36.6 + - - +
204A TRP* 3.1 10.7 + - - +
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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