Contacts of the strand formed by residues 168 - 174 (chain F) in PDB entry 4GG6
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 VAL 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F HIS* 5.4 0.8 + - - -
136F PRO* 4.8 2.2 - - + -
163F PHE* 3.6 42.0 - - + -
166F ASP 3.0 12.6 + - - +
167F HIS* 1.3 75.2 - - - +
169F GLU* 1.3 67.9 + - - +
170F LEU 4.3 0.5 + - - -
189F PRO* 4.3 6.5 - - + -
203F LEU* 4.0 18.9 - - + +
225F VAL* 3.2 35.7 - - + -
226F GLN 3.3 9.6 - - - +
227F PHE* 4.4 7.2 - - + -
228F TYR* 4.4 1.0 - - - -
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Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F HIS* 5.3 5.3 - - - +
168F VAL* 1.3 78.9 - - - +
170F LEU* 1.3 61.4 + - - +
171F SER* 4.0 2.2 + - - -
224F GLN 3.8 0.7 - - - +
225F VAL* 3.3 3.2 - - - -
226F GLN* 2.6 51.7 + - + +
228F TYR* 2.7 38.1 + - + -
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F CYS* 4.5 4.9 - - - -
160F ALA* 5.0 2.2 - - + -
168F VAL 4.2 1.4 + - - -
169F GLU* 1.3 72.4 - - - +
171F SER* 1.3 65.4 + - - +
172F TRP* 3.7 19.1 - - + +
185F THR* 4.8 8.5 + - + +
203F LEU* 4.0 37.3 - - + +
204F SER 4.7 0.4 - - - -
205F SER* 3.7 36.3 - - - +
223F CYS* 3.7 17.7 - - - -
224F GLN 3.3 8.7 - - - +
225F VAL* 3.9 18.6 - - + +
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Residues in contact with SER 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F GLU* 4.0 2.0 + - - -
170F LEU* 1.3 77.7 - - - +
172F TRP* 1.3 63.0 + - - +
173F TRP* 2.8 28.3 + - - -
178F GLU* 3.9 20.0 - - - -
223F CYS* 3.8 2.3 - - - -
224F GLN* 2.8 53.4 + - - +
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Residues in contact with TRP 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.8 5.6 - - + -
156F LEU* 4.0 28.7 - - + -
157F VAL 4.3 0.9 - - - -
158F CYS* 3.4 42.6 - - + -
170F LEU* 3.7 11.1 - - + +
171F SER* 1.3 70.1 - - - +
173F TRP* 1.3 62.5 + - - +
178F GLU* 3.3 10.7 + - - +
179F VAL* 2.9 45.4 + - + +
183F VAL* 3.6 30.2 - - + +
205F SER* 2.8 34.8 + - - -
206F ARG 3.8 3.4 + - - -
207F LEU* 3.5 35.7 - - + -
221F PHE* 5.1 2.2 - - + -
222F ARG 3.9 14.1 - - - -
223F CYS* 3.8 17.5 - - + -
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Residues in contact with TRP 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F SER* 2.8 29.8 + - - -
172F TRP* 1.3 80.0 - - - +
174F VAL* 1.3 63.3 + - - +
175F ASN 4.1 0.4 + - - -
176F GLY* 3.4 34.3 - - - +
177F LYS* 4.1 2.7 - - - -
178F GLU* 3.5 42.0 - - + -
220F HIS 3.9 0.3 - - - +
221F PHE* 3.5 2.1 - - - -
222F ARG* 2.7 68.4 + - + +
224F GLN* 3.3 38.5 + - + -
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F TRP 4.3 0.2 - - - -
173F TRP* 1.3 74.2 - - - +
175F ASN* 1.3 87.0 - - - +
176F GLY 3.3 1.3 - - - -
177F LYS* 3.0 23.1 + - - +
179F VAL* 3.7 31.6 - - + +
207F LEU* 4.0 8.5 - - + -
209F VAL* 5.5 2.5 - - + -
213F PHE* 3.9 28.0 - - + -
219F ASN* 5.2 0.2 - - - +
220F HIS 3.4 11.7 - - - +
221F PHE* 3.7 26.5 - - + -
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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