Contacts of the strand formed by residues 211 - 217 (chain W) in PDB entry 6G0L
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 TYR 211 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186W ARG 3.6 5.6 - - - +
187W LEU* 4.0 17.7 - - + -
188W LYS* 3.5 8.8 - - - +
202W PRO* 3.8 25.2 - - + +
206W ASN* 3.8 4.7 + - + +
207W CYS* 2.5 67.9 + - - +
210W ASN* 1.3 110.6 + - + +
212W GLU* 1.3 58.7 + - - +
213W PHE* 3.6 21.4 - - + -
229W THR* 3.7 13.3 + - - +
249W PHE* 3.8 26.9 - + - -
253W ASP* 4.1 5.8 + - - -
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Residues in contact with GLU 212 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W ARG* 2.5 54.5 + - - +
187W LEU* 2.5 29.5 - - - +
188W LYS* 3.6 17.0 - - + +
211W TYR* 1.3 72.2 - - - +
213W PHE* 1.3 62.8 + - - +
227W TRP* 3.4 34.1 - - + +
228W GLU 5.0 0.4 - - - -
229W THR* 4.3 8.7 - - - +
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Residues in contact with PHE 213 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182W VAL* 6.1 2.2 - - + -
184W ASN 3.6 3.8 - - - +
185W HIS* 3.5 29.4 - - + -
186W ARG 5.2 0.4 - - - -
207W CYS* 3.8 26.9 - - + -
211W TYR* 3.6 38.4 - + + -
212W GLU* 1.3 76.8 - - - +
214W LEU* 1.3 65.0 + - - +
215W ILE* 3.3 4.8 + - + +
226W THR 3.3 0.3 - - - +
227W TRP* 3.6 4.0 - - - -
228W GLU 2.9 37.7 + - - +
229W THR* 5.6 2.7 - - + -
230W TYR* 5.3 7.6 - + - -
242W LEU* 4.0 38.4 - - + -
245W TYR* 5.1 7.6 - + - -
246W CYS* 4.6 9.0 - - + -
249W PHE* 4.7 16.8 - + + -
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Residues in contact with LEU 214 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182W VAL* 4.5 4.7 - - - +
183W ILE* 3.3 53.8 + - + -
184W ASN* 2.5 32.1 + - + +
213W PHE* 1.3 71.5 - - - +
215W ILE* 1.3 59.8 + - - +
225W ASN* 3.2 50.5 - - + +
226W THR 3.4 4.5 - - - +
227W TRP* 3.3 42.1 - - + +
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Residues in contact with ILE 215 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179W ILE* 3.3 39.7 - - + -
181W ILE 4.4 4.0 - - - +
182W VAL* 6.5 1.1 - - + -
213W PHE* 3.6 10.5 - - + +
214W LEU* 1.3 74.5 - - - +
216W LYS* 1.3 74.5 + - - +
217W TRP* 3.7 13.0 + - + -
225W ASN* 3.6 5.0 - - - -
226W THR* 2.7 39.3 + - - +
228W GLU* 3.3 41.5 - - + +
229W THR 4.8 1.3 - - - +
233W ILE* 4.1 10.1 - - + -
242W LEU* 4.6 17.5 - - + -
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Residues in contact with LYS 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180W ASP* 3.0 38.8 + - - +
181W ILE* 3.4 42.2 + - - +
183W ILE* 3.3 40.0 - - + +
214W LEU 4.1 1.6 + - - -
215W ILE* 1.3 79.4 - - - +
217W TRP* 1.3 69.0 + - - +
220W GLU 4.6 4.0 - - - +
221W SER 4.5 4.9 - - - +
222W HIS* 3.2 58.8 + - + +
224W HIS 5.9 0.7 - - - +
225W ASN* 4.8 6.3 - - + +
281W PHE* 5.1 4.4 - - - -
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Residues in contact with TRP 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177W HIS* 2.6 51.0 - + + +
178W GLY* 3.2 37.7 - - - -
179W ILE* 3.1 34.3 - - + -
180W ASP* 3.5 7.0 - - - +
215W ILE* 3.7 8.4 + - + -
216W LYS* 1.3 79.2 - - - +
218W THR* 1.3 65.8 + - - +
220W GLU* 3.5 28.2 + - + +
224W HIS* 4.1 20.8 + - + +
226W THR* 3.4 29.1 + - + +
228W GLU* 5.2 0.4 - - + -
233W ILE* 3.5 32.8 - - + -
236W VAL* 3.8 15.7 - - + -
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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