Contacts of the strand formed by residues 179 - 185 (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 LEU 179 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143I VAL* 3.6 35.9 - - + +
144I PHE 4.2 2.5 - - - -
145I PHE* 3.6 32.8 - - + -
164I ALA* 3.3 3.6 - - - +
165I LEU* 2.6 49.5 + - + +
177I ALA* 3.4 2.5 - - - +
178I ALA* 1.3 78.1 - - - +
180I ALA* 1.3 61.1 + - - +
200I GLN* 3.6 27.1 - - + +
201I GLY* 4.3 3.8 - - - -
202I ARG* 3.6 35.0 - - + +
204I LEU* 4.9 4.3 - - + -
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Residues in contact with ALA 180 (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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148G GLU* 5.3 10.8 - - - +
197G PHE* 5.3 2.1 - - - -
145I PHE* 4.9 1.3 - - - -
163I LEU 3.2 8.1 - - - +
164I ALA* 4.9 3.4 - - + -
177I ALA* 4.9 12.8 - - + +
179I LEU* 1.3 78.4 - - - +
181I LEU* 1.3 63.2 + - - +
182I THR* 5.9 0.7 - - - +
200I GLN* 3.5 28.7 + - - +
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Residues in contact with LEU 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G PHE* 3.5 35.2 - - + -
145I PHE* 3.8 27.1 - - + +
147I LEU* 4.5 14.8 - - + -
161I VAL 4.6 0.4 - - - -
162I SER* 3.2 6.1 - - - -
163I LEU* 2.7 47.2 + - + +
180I ALA* 1.3 72.0 - - - +
182I THR* 1.3 78.8 + - - +
183I VAL* 5.0 2.5 - - + -
198I GLY* 3.8 30.3 - - - +
199I PHE 3.8 7.9 - - - +
200I GLN* 3.5 15.3 - - + +
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Residues in contact with THR 182 (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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193G ARG* 3.9 27.2 + - - +
195G SER* 5.1 16.7 - - - -
197G PHE* 5.3 10.8 - - - +
160I SER* 4.1 15.0 - - - +
161I VAL 3.7 3.1 - - - +
162I SER* 3.9 18.2 + - - +
180I ALA* 5.9 0.7 - - - +
181I LEU* 1.3 87.1 + - - +
183I VAL* 1.3 65.8 + - - +
184I ASP 4.2 0.9 + - - -
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Residues in contact with VAL 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G ARG* 4.4 2.9 - - - -
147I LEU* 3.7 30.1 - - + +
149I LEU* 3.8 11.9 - - + -
160I SER* 3.5 4.3 - - - -
161I VAL* 3.0 37.0 + - + +
181I LEU* 5.0 3.4 - - + -
182I THR* 1.3 78.7 - - - +
184I ASP* 1.3 62.8 + - - +
185I LEU* 3.9 3.0 + - + +
196I ALA* 3.6 29.6 - - + -
197I PHE 3.6 33.2 - - - +
198I GLY* 3.9 8.5 - - - +
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Residues in contact with ASP 184 (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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191G GLU* 3.7 7.1 - - - +
193G ARG* 3.6 46.0 + - - +
159I GLY 3.6 7.2 - - - +
182I THR 4.2 0.8 + - - -
183I VAL* 1.3 73.9 - - - +
185I LEU* 1.3 77.1 + - - +
186I PRO* 3.8 10.2 - - - +
196I ALA* 3.5 20.8 - - - +
197I PHE 5.5 0.2 + - - -
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Residues in contact with LEU 185 (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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191G GLU* 3.7 5.7 - - - +
102I LEU* 4.9 2.9 - - + -
149I LEU* 3.8 12.1 - - + -
158I SER* 3.7 4.8 - - - -
159I GLY 2.8 43.5 + - - +
161I VAL* 3.8 23.6 - - + -
183I VAL* 4.5 3.8 - - + +
184I ASP* 1.3 89.2 + - - +
186I PRO* 1.3 67.2 - - - +
187I PRO* 3.8 0.7 - - - +
196I ALA* 3.8 8.7 - - + -
220I ALA* 5.1 5.6 - - + -
226I TRP* 3.6 65.5 - - + +
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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