Contacts of the strand formed by residues 195 - 206 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148I GLU* 5.7 4.8 + - - -
149I LEU 3.5 6.8 + - - -
150I ARG* 5.4 2.3 - - - +
186I PRO* 4.9 1.7 - - - +
193I ARG* 2.7 47.6 + - - +
194I ASN* 1.3 83.5 + - - +
196I ALA* 1.3 61.5 + - - +
197I PHE* 6.3 0.2 - - - -
226I TRP* 4.4 4.0 - - - -
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Residues in contact with ALA 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I GLU* 3.4 8.8 - - - +
149I LEU* 3.0 28.3 + - + -
183I VAL* 3.6 11.2 - - + -
184I ASP 3.5 24.7 - - - +
185I LEU* 3.8 15.5 - - + -
186I PRO* 4.8 1.3 - - + -
193I ARG* 4.6 2.7 - - - +
195I SER* 1.3 75.2 - - - +
197I PHE* 1.3 67.5 + - - +
226I TRP* 4.0 8.9 - - + -
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Residues in contact with PHE 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLN* 5.0 15.7 - - + -
147I LEU 3.1 20.0 - - - -
148I GLU* 4.2 23.1 - - + -
183I VAL* 3.6 17.7 - - - +
184I ASP 5.5 0.3 + - - -
193I ARG* 5.9 2.2 - - - +
195I SER* 6.3 0.4 - - - -
196I ALA* 1.3 79.9 - - - +
198I GLY* 1.3 88.8 + - - +
199I PHE* 4.1 17.0 - + + -
232I ALA 5.8 0.9 - - - -
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Residues in contact with GLY 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLN* 3.8 2.1 - - - -
147I LEU 2.9 27.8 + - - +
181I LEU* 3.8 12.3 - - - -
182I THR 5.8 0.4 - - - -
183I VAL* 3.9 11.2 - - - +
197I PHE* 1.3 91.5 - - - +
199I PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G TYR* 5.6 1.6 - - - -
197G PHE* 3.0 21.4 - - - -
199G PHE* 3.5 50.7 - + + +
142I TYR* 4.5 5.2 - + - -
144I PHE* 3.6 31.4 - + + -
145I PHE 3.1 21.3 - - - -
146I GLN* 3.7 27.8 - - + -
181I LEU* 3.8 4.6 - - - +
197I PHE* 4.1 16.3 - + + -
198I GLY* 1.3 74.6 - - - +
200I GLN* 1.3 68.0 + - - +
201I GLY 4.5 0.2 - - - -
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Residues in contact with GLN 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G GLN* 2.7 35.4 + - - +
148G GLU* 5.2 5.7 + - - -
197G PHE* 3.0 28.9 - - + -
199G PHE* 3.8 2.0 - - - -
232G ALA* 5.3 2.8 + - - +
144I PHE* 3.1 2.3 - - - +
145I PHE* 2.5 41.9 + - + +
179I LEU* 3.6 25.2 - - + +
180I ALA* 3.5 23.8 + - - +
181I LEU* 3.5 22.1 - - + +
199I PHE* 1.3 82.5 - - - +
201I GLY* 1.3 68.3 + - - +
202I ARG* 4.7 1.8 - - - +
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Residues in contact with GLY 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G PHE* 4.0 1.6 - - - -
146G GLN* 3.4 9.0 + - - -
199G PHE* 3.0 29.9 - - - -
142I TYR* 4.5 8.1 - - - -
143I VAL 3.2 13.2 - - - -
144I PHE* 3.9 7.4 - - - -
179I LEU* 4.3 2.0 - - - -
200I GLN* 1.3 83.7 + - - +
202I ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G GLN* 3.4 27.7 - - - +
117G GLY* 3.6 22.4 - - - -
144G PHE* 3.8 9.0 - - - -
146G GLN* 3.2 34.5 + - - +
231G GLY 3.9 12.4 + - - -
232G ALA* 5.9 1.2 - - - +
234G VAL* 3.8 15.1 - - - +
142I TYR* 4.4 6.8 - - - -
143I VAL 3.2 23.3 + - - +
178I ALA* 3.1 23.1 + - - +
179I LEU* 3.6 24.7 - - + -
200I GLN* 4.7 1.1 - - - +
201I GLY* 1.3 68.5 - - - -
203I LEU* 1.3 65.2 + - - +
204I LEU* 3.4 30.9 + - + +
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Residues in contact with LEU 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G PHE* 4.5 8.3 - - + -
93G ALA 3.2 33.0 - - - +
94G GLN* 2.9 39.1 + - + +
119G SER* 5.9 3.0 - - - -
144G PHE* 3.8 13.1 - - + -
237G LEU 3.3 23.1 - - - +
238G PHE* 4.0 12.3 - - + -
140I VAL* 4.4 14.1 - - + -
141I TYR 3.7 4.3 - - - +
142I TYR* 4.1 10.3 - - + -
202I ARG* 1.3 70.8 - - - +
204I LEU* 1.3 62.7 + - - +
240I VAL* 3.7 32.1 - - + -
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Residues in contact with LEU 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I VAL* 3.4 9.0 - - - +
141I TYR* 2.8 37.8 + - - +
143I VAL* 3.9 31.9 - - + -
165I LEU* 4.5 10.5 - - + -
167I LEU* 6.0 0.9 - - + -
178I ALA* 4.1 29.2 - - + +
179I LEU* 4.9 4.7 - - + -
202I ARG* 3.4 43.5 + - + +
203I LEU* 1.3 78.2 - - - +
205I HIS* 1.3 65.1 + - - +
206I LEU* 3.8 13.9 + - + -
212I LEU* 5.7 0.2 - - + -
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Residues in contact with HIS 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G SER* 6.5 0.9 - - - -
39H ASN* 4.0 31.5 - - + +
60H ARG* 3.6 32.7 + - + +
61H THR* 6.1 2.4 - - - +
139I GLY* 4.0 13.2 + - - -
140I VAL* 4.6 14.6 - - + +
167I LEU* 4.6 9.4 - - - +
204I LEU* 1.3 74.0 - - - +
206I LEU* 1.3 67.8 + - - +
207I SER* 4.1 8.5 - - - -
210I GLN* 5.0 0.7 + - - -
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Residues in contact with LEU 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I VAL* 3.8 24.2 - - + -
138I ALA* 3.5 2.0 - - - +
139I GLY 2.9 31.7 + - - +
141I TYR* 3.5 42.4 - - + -
143I VAL* 4.5 4.0 - - + -
167I LEU* 3.9 31.0 - - + -
204I LEU* 3.8 15.5 + - + +
205I HIS* 1.3 86.9 + - - +
207I SER* 1.3 65.9 + - - +
210I GLN* 4.0 7.4 - - + +
212I LEU* 4.0 15.5 - - + -
237I LEU* 4.3 9.4 - - + -
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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