Contacts of the strand formed by residues 179 - 185 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G VAL* 4.1 33.4 - - + +
145G PHE* 3.4 28.3 - - + -
164G ALA* 3.4 2.8 - - - -
165G LEU* 3.1 40.2 + - + -
177G ALA* 3.2 10.6 + - - +
178G ALA* 1.3 84.0 - - - +
180G ALA* 1.3 68.7 + - - +
200G GLN* 4.0 14.6 - - + +
202G ARG* 3.5 38.1 - - + +
204G LEU* 4.2 9.9 - - + -
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Residues in contact with ALA 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G PHE* 4.0 3.7 - - - -
163G LEU 3.1 17.3 - - - +
164G ALA* 4.1 4.3 - - + +
177G ALA* 5.1 4.5 - - + -
179G LEU* 1.3 82.1 - - - +
181G LEU* 1.3 62.8 + - - +
182G THR* 6.0 0.4 - - - +
200G GLN* 3.1 31.2 + - - +
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Residues in contact with LEU 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G PHE* 3.8 17.0 - - + -
147G LEU* 4.8 10.8 - - + -
162G SER* 3.2 6.8 - - - -
163G LEU* 3.0 40.5 + - + +
180G ALA* 1.3 75.3 - - - +
182G THR* 1.3 84.9 + - - +
183G VAL* 3.6 24.7 - - + -
198G GLY* 3.6 34.1 - - - +
199G PHE 4.3 3.6 - - - +
200G GLN* 3.6 30.1 - - + +
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Residues in contact with THR 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G SER* 4.5 17.5 - - - -
161G VAL 3.6 4.5 - - - +
162G SER* 3.7 16.0 + - - +
180G ALA* 6.0 0.5 - - - +
181G LEU* 1.3 85.5 + - - +
183G VAL* 1.3 65.1 + - - +
184G ASP* 4.1 2.0 + - + +
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Residues in contact with VAL 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G LEU* 3.7 27.8 - - + +
149G LEU* 3.9 12.8 - - + -
160G SER* 3.6 1.3 - - - -
161G VAL* 2.9 36.3 + - - +
181G LEU* 3.6 24.5 - - + -
182G THR* 1.3 73.2 - - - +
184G ASP* 1.3 63.9 + - - +
185G LEU* 3.8 0.5 + - - +
196G ALA* 3.6 30.3 - - + -
197G PHE 3.8 12.8 - - - +
198G GLY* 3.7 19.5 - - - +
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Residues in contact with ASP 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G GLY 3.8 9.7 - - - +
160G SER* 4.2 10.6 + - - +
182G THR* 4.1 2.9 + - + +
183G VAL* 1.3 74.7 - - - +
185G LEU* 1.3 73.4 + - - +
186G PRO* 3.3 13.9 - - - +
187G PRO* 5.4 0.9 - - - +
196G ALA* 3.3 20.3 - - - +
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Residues in contact with LEU 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 4.5 3.1 - - + -
149G LEU* 4.1 17.3 - - + -
158G SER* 3.7 4.9 - - - -
159G GLY* 2.7 45.5 + - - +
161G VAL* 3.7 32.5 - - + -
183G VAL 4.6 1.3 - - - +
184G ASP* 1.3 82.1 + - - +
186G PRO* 1.3 68.5 - - - +
187G PRO* 3.6 3.1 - - - +
196G ALA* 4.3 3.4 - - + -
220G ALA* 4.6 7.2 - - + -
226G TRP* 3.5 61.5 - - + +
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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