Contacts of the strand formed by residues 164 - 171 (chain L) in PDB entry 6DF3
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 PHE 164 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H ARG* 5.0 17.0 - - - -
162L ASP 3.6 13.7 - - - +
163L LEU* 1.3 80.0 - - - +
165L TYR* 1.3 81.2 + - - +
166L HIS* 4.6 6.3 - - + -
180L GLY* 5.3 1.1 - - - -
181L GLY* 3.3 24.2 - - - +
182L LYS* 4.4 4.0 - - + +
203L ILE* 3.6 3.6 - - - -
204L CYS* 2.8 68.2 + - + +
206L PRO* 3.8 23.6 - - + -
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Residues in contact with TYR 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L PRO* 5.2 0.2 - - + -
139L VAL* 3.7 40.1 - - + +
140L HIS 4.8 1.0 + - - -
141L PRO* 4.9 0.3 - - - +
157L GLU* 2.4 41.3 + - + +
163L LEU* 3.7 21.5 - - + -
164L PHE* 1.3 84.0 - - - +
166L HIS* 1.3 60.5 + - - +
167L LEU* 3.8 17.9 - - + -
180L GLY* 3.0 24.8 - - - -
181L GLY 2.8 15.8 + - - +
182L LYS* 3.7 12.3 - - - -
183L GLN 3.2 28.7 - - - -
184L ARG* 4.4 9.6 + - + +
186L TYR* 4.5 0.7 - - - +
201L ILE* 4.8 3.1 - - + -
202L MET 3.4 7.0 - - - +
203L ILE* 3.9 22.4 - - + -
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Residues in contact with HIS 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ARG* 3.3 30.9 + - + +
164L PHE* 4.3 6.3 + - + -
165L TYR* 1.3 73.3 - - - +
167L LEU* 1.3 64.2 + - - +
168L GLU* 2.6 40.4 + - + +
178L HIS* 3.7 30.8 - + + +
179L LEU 3.8 6.3 + - - -
180L GLY* 4.5 0.4 - - - -
200L THR 3.9 0.9 - - - +
201L ILE* 3.4 3.3 - - - +
202L MET* 2.9 52.9 + - + +
204L CYS* 4.0 19.5 - - - -
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Residues in contact with LEU 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L MET* 3.7 34.8 - - + -
139L VAL* 4.7 3.1 - - + -
165L TYR* 3.8 18.2 - - + +
166L HIS* 1.3 79.8 + - - +
168L GLU* 1.3 62.8 + - - +
177L MET 3.9 0.2 - - - +
178L HIS* 3.5 4.3 - - - -
179L LEU* 2.9 39.1 + - + +
186L TYR* 3.7 51.4 - - + -
188L PHE* 4.0 14.6 - - + -
200L THR 3.5 4.3 - - - -
201L ILE* 3.7 20.0 - - + -
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Residues in contact with GLU 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188H ILE* 5.7 1.9 - - - +
137L MET* 4.9 1.2 - - - +
166L HIS* 2.6 39.8 + - + +
167L LEU* 1.3 74.5 - - - +
169L LEU* 1.3 60.1 + - - +
170L GLN 4.1 0.7 - - - +
176L GLN* 3.9 26.0 + - + +
177L MET 3.3 8.3 - - - +
178L HIS* 3.9 12.2 + - + -
188L PHE* 4.3 3.9 - - - -
198L LEU 3.6 1.1 - - - +
199L GLY* 3.3 4.5 - - - -
200L THR* 2.9 50.4 + - - +
202L MET* 5.6 5.0 - - - +
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Residues in contact with LEU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ILE* 4.1 9.6 - - + -
137L MET* 3.9 26.0 - - + -
168L GLU* 1.3 72.1 - - - +
170L GLN* 1.3 63.9 + - - +
171L VAL* 3.6 4.1 + - + +
176L GLN* 3.4 5.8 - - - -
177L MET* 2.9 37.7 + - + -
188L PHE* 3.8 41.5 - - + -
191L LEU* 3.9 25.8 - - + -
197L PHE* 3.8 34.5 - - + -
198L LEU 3.4 7.6 - - - +
199L GLY* 4.1 3.4 - - - +
219L VAL* 5.6 1.3 - - + -
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Residues in contact with GLN 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L GLU* 4.1 1.4 - - + +
169L LEU* 1.3 71.1 - - - +
171L VAL* 1.3 62.7 + - - +
172L ASN 4.2 14.4 - - - +
173L ARG* 4.0 27.5 + - + +
174L THR 5.5 0.4 - - - -
175L TYR 3.7 7.3 + - - +
176L GLN* 4.0 26.2 - - + +
196L GLU 4.8 0.5 - - - +
197L PHE* 3.8 11.1 - - - -
198L LEU* 3.0 53.1 + - + +
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Residues in contact with VAL 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H ASP* 5.5 1.1 - - - +
151H HIS* 6.0 2.0 - - + +
169L LEU* 3.8 12.3 - - + +
170L GLN* 1.3 76.9 - - - +
172L ASN* 1.3 75.9 + - + +
173L ARG* 3.5 1.2 - - - -
174L THR* 3.1 16.3 + - - -
175L TYR* 3.0 58.3 + - + +
177L MET* 4.0 19.7 - - + -
191L LEU* 5.4 0.9 - - + -
195L THR* 6.3 0.4 - - + -
197L PHE* 3.9 29.6 - - + -
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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