Contacts of the strand formed by residues 190 - 197 (chain G) in PDB entry 3WBR
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 GLU 190 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C HIS* 3.0 11.3 - - - -
185G PHE* 3.5 31.6 - - + -
186G ARG 2.5 42.9 + - - -
188G SER 4.7 7.0 - - - +
189G GLU* 1.3 78.6 - - - +
191G TRP* 1.3 67.7 + - + +
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Residues in contact with TRP 191 (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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167C PHE* 4.7 1.0 - - - +
169C HIS* 3.5 3.4 + - - -
127G GLN* 4.8 5.0 + - - +
131G ILE* 3.4 53.8 + - + +
134G LEU* 3.5 38.4 - - + -
135G LYS 3.3 24.0 - - - -
136G ARG* 3.5 34.1 - - + +
138G SER 4.2 5.2 - - - -
183G ILE* 4.1 10.5 - - + -
184G ASN* 3.4 39.9 - - - -
185G PHE* 3.8 18.9 - + + -
189G GLU 4.0 5.5 - - - +
190G GLU* 1.3 87.7 - - + +
192G GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 192 (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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167C PHE 3.2 13.0 - - - -
169C HIS* 3.2 25.4 + - - -
127G GLN* 4.6 3.4 - - - -
183G ILE* 3.3 6.5 - - - +
184G ASN 3.1 26.3 + - - -
191G TRP* 1.3 76.6 - - - +
193G TRP* 1.3 69.1 + - - -
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Residues in contact with TRP 193 (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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155C TRP* 3.7 23.8 - + - -
161C TYR* 4.8 0.2 - + - -
165C VAL 4.2 4.3 - - - -
166C THR* 3.7 33.4 - - + -
167C PHE* 2.8 43.5 + + + +
168C TRP* 3.4 37.9 - + + -
169C HIS 2.9 20.0 + - - +
172C GLU* 3.7 3.3 - - - +
121G ILE* 4.0 19.8 - - + +
127G GLN* 3.0 24.7 + - - +
142G LEU* 3.7 23.1 - - + +
144G LEU* 3.8 24.0 - - + -
181G ALA* 4.9 0.2 - - + -
182G ILE 3.1 8.1 - - - +
183G ILE* 4.0 11.2 - - + +
192G GLY* 1.3 79.1 - - - -
194G ASN* 1.3 65.0 + - - +
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Residues in contact with ASN 194 (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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168C TRP* 3.6 4.7 - - - -
169C HIS* 2.9 19.4 - - - -
172C GLU* 3.7 13.3 - - - +
181G ALA* 3.3 4.5 - - - -
182G ILE* 2.8 48.7 + - + +
184G ASN* 2.6 37.5 + - - +
186G ARG* 2.7 33.2 + - - -
192G GLY 3.9 1.2 + - - -
193G TRP* 1.3 72.2 - - - +
195G ASP* 1.3 61.5 + - - +
196G ILE* 4.8 3.8 - - + -
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Residues in contact with ASP 195 (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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151C ARG* 5.2 1.2 - - - -
153C TRP* 3.5 31.7 - - + -
168C TRP* 3.8 9.8 - - + -
172C GLU* 3.1 18.7 + - - +
173C PRO* 3.3 12.2 - - - +
174C ASN* 3.1 29.5 + - - +
179G ARG* 2.8 46.9 + - + +
180G CYS 3.4 3.4 - - - -
194G ASN* 1.3 74.1 - - - +
196G ILE* 1.3 60.4 + - - +
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Residues in contact with ILE 196 (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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200A VAL* 3.8 39.5 - - + -
141G PHE* 3.8 11.2 - - + -
179G ARG* 3.5 15.0 + - - +
180G CYS 2.9 37.8 + - - +
182G ILE* 3.7 44.6 - - + -
194G ASN* 4.8 3.1 - - + -
195G ASP* 1.3 80.6 - - - +
197G HIS* 1.3 74.2 + - - +
200G VAL* 4.1 7.4 - - + -
202G GLN* 3.9 13.0 - - + -
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Residues in contact with HIS 197 (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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200A VAL* 5.7 0.2 - - - +
177G ASP* 2.8 33.1 + - + -
178G GLU* 4.0 28.0 - - + -
179G ARG* 3.9 13.8 - - - +
196G ILE* 1.3 89.7 - - - +
198G CYS* 1.3 78.5 + - - +
199G HIS* 2.7 48.9 + + + +
200G VAL* 3.3 17.3 + - + +
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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