Contacts of the strand formed by residues 195 - 206 (chain E) in PDB entry 6A3V
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 SER 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C THR* 4.7 18.1 + - - -
148E GLU* 5.1 11.3 + - - -
149E LEU 3.4 7.0 - - - -
150E ARG* 5.3 2.9 - - - +
193E ARG* 2.5 45.2 + - - +
194E ASN* 1.3 82.9 + - - +
196E ALA* 1.3 56.3 - - - +
197E PHE* 5.5 1.3 - - - -
226E TRP* 4.8 2.0 - - - -
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Residues in contact with ALA 196 (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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147E LEU 4.0 0.3 - - - +
148E GLU* 3.2 3.7 - - - +
149E LEU* 2.6 41.3 + - + +
183E VAL* 3.5 22.7 - - + -
184E ASP 3.7 14.8 - - - +
185E LEU* 4.0 15.5 - - + -
186E PRO* 4.7 2.5 - - + -
193E ARG* 4.4 2.2 - - - +
195E SER* 1.3 74.1 - - - +
197E PHE* 1.3 61.9 + - - +
226E TRP* 4.1 10.7 - - + -
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Residues in contact with PHE 197 (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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180C ALA 5.6 0.2 - - - -
181C LEU* 4.1 24.2 - - + -
182C THR* 4.8 15.9 - - - +
198C GLY* 5.8 0.7 - - - -
199C PHE 3.1 28.7 - - - -
200C GLN* 3.1 36.1 - - + -
146E GLN* 4.2 11.4 - - + -
147E LEU 3.3 14.1 - - - -
148E GLU* 4.1 21.3 - - + -
183E VAL* 3.8 10.9 - - - +
193E ARG* 5.0 5.5 - - - +
195E SER* 4.3 2.4 + - - -
196E ALA* 1.3 76.2 - - - +
198E GLY* 1.3 80.6 + - - +
199E PHE* 4.0 4.9 - - + -
232E ALA 5.7 0.4 - - - -
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Residues in contact with GLY 198 (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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146E GLN* 3.9 1.0 - - - -
147E LEU 3.0 30.4 + - - -
181E LEU* 3.7 11.4 - - - +
182E THR 5.5 1.3 - - - -
183E VAL* 3.7 12.7 - - - +
197E PHE* 1.3 89.1 - - - +
199E PHE* 1.3 60.0 + - - -
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Residues in contact with PHE 199 (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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197A PHE* 3.2 22.8 - - - -
199A PHE* 3.6 37.4 - + + +
142C TYR* 3.5 22.0 - - - -
199C PHE* 3.3 41.3 - + + +
200C GLN* 3.9 2.0 - - - -
201C GLY 3.0 35.2 - - - -
142E TYR* 4.7 0.4 - - - -
144E PHE* 3.7 19.3 - + + -
145E PHE 3.1 20.6 - - - -
146E GLN* 3.5 15.9 - - + -
181E LEU* 3.5 4.5 - - - +
197E PHE* 4.0 1.7 - - + -
198E GLY* 1.3 74.6 - - - +
200E GLN* 1.3 78.8 + - - +
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Residues in contact with GLN 200 (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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146A GLN* 3.0 24.6 + - - +
148A GLU* 5.3 1.4 + - - -
197A PHE* 3.1 31.4 - - + -
199A PHE* 4.5 3.4 - - - -
232A ALA* 5.8 0.6 + - - +
144E PHE* 3.2 4.0 - - - +
145E PHE* 2.6 40.0 + - + +
178E ALA 5.1 0.4 + - - -
179E LEU* 4.3 10.2 - - + +
180E ALA 2.7 43.1 + - - +
181E LEU* 3.5 15.9 - - + +
199E PHE* 1.3 87.3 - - - +
201E GLY* 1.3 61.1 + - - +
202E ARG* 4.1 10.5 - - - +
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Residues in contact with GLY 201 (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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144A PHE* 3.8 2.4 - - - -
146A GLN* 3.7 7.3 + - - -
199A PHE* 3.1 27.7 - - - -
142E TYR* 4.1 11.9 - - - -
143E VAL 3.2 14.1 - - - -
144E PHE* 3.8 7.2 - - - -
179E LEU* 4.5 1.8 - - - -
200E GLN* 1.3 80.8 - - - +
202E ARG* 1.3 67.3 + - - +
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Residues in contact with ARG 202 (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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94A GLN* 3.6 19.7 - - - +
96A VAL* 4.6 3.8 - - - +
117A GLY* 4.9 7.5 - - - -
144A PHE* 3.6 9.6 - - + -
146A GLN* 3.2 36.5 + - - +
231A GLY 3.4 17.1 + - - -
232A ALA* 5.1 3.4 + - - +
234A VAL* 3.3 24.9 - - - +
142E TYR* 4.0 9.0 - - - -
143E VAL* 3.1 25.2 + - - +
178E ALA* 2.8 29.7 + - - +
179E LEU* 3.6 23.4 - - + +
200E GLN* 4.1 9.4 - - - +
201E GLY* 1.3 72.4 - - - +
203E LEU* 1.3 71.2 + - - +
204E LEU* 3.6 12.4 + - - +
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Residues in contact with LEU 203 (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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92A PHE* 3.8 23.6 - - + -
93A ALA 3.4 28.9 - - - +
94A GLN* 2.9 32.9 + - + +
117A GLY 5.0 0.7 - - - +
119A SER* 5.7 2.7 - - - +
144A PHE* 3.5 12.6 - - + -
237A LEU 3.6 13.2 - - - +
238A PHE* 4.2 7.4 - - + -
140E VAL* 4.1 9.2 - - + -
141E TYR 3.5 3.1 - - - +
142E TYR* 3.8 20.2 - - + -
202E ARG* 1.3 74.0 - - - +
204E LEU* 1.3 68.6 + - - +
240E VAL* 3.7 30.3 - - + -
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Residues in contact with LEU 204 (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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94A GLN* 5.7 0.2 - - - +
117A GLY* 6.4 2.2 - - - -
119A SER* 6.0 0.4 - - - -
140E VAL* 3.2 7.3 - - - -
141E TYR* 2.8 41.8 + - - +
143E VAL* 4.0 17.5 - - + -
165E LEU* 3.7 20.2 - - + -
167E LEU* 5.4 4.9 - - + -
178E ALA* 4.1 21.5 - - + -
179E LEU* 3.6 29.4 - - + -
202E ARG* 4.2 13.2 - - - +
203E LEU* 1.3 81.2 - - - +
205E HIS* 1.3 61.5 + - - +
206E LEU* 3.7 19.0 + - + +
212E LEU* 5.1 0.2 - - + -
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Residues in contact with HIS 205 (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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119A SER* 5.1 9.0 + - - +
39B ASN* 4.8 22.6 + - + +
60B ARG* 5.5 13.4 + - + -
138E ALA* 5.3 3.8 - - + +
139E GLY* 3.2 23.3 + - - -
140E VAL* 3.8 16.5 - - + +
167E LEU* 4.9 5.7 - - - +
204E LEU* 1.3 72.3 - - - +
206E LEU* 1.3 75.9 + - - +
207E SER* 5.1 6.7 + - - -
210E GLN* 4.8 3.6 + - - -
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Residues in contact with LEU 206 (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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135E VAL* 3.7 28.3 - - + -
138E ALA* 3.2 4.5 - - - +
139E GLY 2.9 29.5 + - - +
141E TYR* 3.6 35.4 - - + -
143E VAL* 4.8 2.7 - - + -
167E LEU* 4.1 20.2 - - + -
204E LEU* 3.7 16.5 + - + +
205E HIS* 1.3 88.0 - - - +
207E SER* 1.3 63.1 + - - +
210E GLN* 4.2 6.7 - - + +
212E LEU* 3.9 32.8 - - + -
237E LEU* 4.1 8.3 - - + -
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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