Contacts of the strand formed by residues 165 - 172 (chain C) in PDB entry 5YL4
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 SER 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLN* 3.3 22.9 + - - +
134C GLY* 3.1 4.2 - - - -
135C PHE* 2.8 26.7 + - - -
163C LYS 3.4 2.2 + - - -
164C LYS* 1.3 78.2 - - - +
166C LYS* 1.3 61.3 + - - +
167C LEU* 4.2 14.9 - - - +
199C ASP* 3.2 16.2 - - - -
253C THR* 6.0 1.6 - - - +
256C GLN* 5.3 4.7 + - - -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.6 18.4 - - + -
137C VAL* 5.3 0.7 - - + -
154C MET* 3.5 40.6 - - + -
157C LEU* 3.7 32.1 + - + -
158C SER* 3.0 32.3 + - - +
161C TYR* 6.5 0.2 - - + -
162C GLY 4.7 3.0 + - - -
164C LYS 3.8 11.4 + - - +
165C SER* 1.3 79.6 - - - +
167C LEU* 1.3 64.4 + - - +
197C HIS* 3.1 29.6 + - - +
198C SER* 3.4 5.4 + - - -
199C ASP* 2.9 37.8 + - - +
200C CYS 3.7 1.2 + - - -
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE 3.0 7.2 + - - +
136C LEU* 3.4 32.6 - - + -
137C VAL* 2.8 35.6 + - - +
165C SER* 4.5 15.0 - - - +
166C LYS* 1.3 80.9 - - - +
168C GLU* 1.3 58.1 + - - +
169C PHE* 5.5 3.6 - - + -
199C ASP* 4.7 1.6 - - + -
200C CYS* 3.1 22.4 - - + +
202C PHE* 4.5 12.8 - - + -
242C LEU* 6.1 0.2 - - + -
252C LEU* 3.9 27.4 - - + -
256C GLN* 3.7 31.0 - - - +
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Residues in contact with GLU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 3.3 11.4 - - + +
139C HIS* 2.9 29.9 + - + +
141C PHE* 4.9 3.3 - - - -
150C THR* 4.8 0.5 - - - +
154C MET* 4.0 11.9 - - + -
167C LEU* 1.3 75.9 - - - +
169C PHE* 1.3 64.4 + - - +
170C SER* 3.5 16.1 + - - +
194C THR* 3.4 25.2 - - - +
198C SER* 2.9 30.7 + - - +
200C CYS 2.9 7.1 + - - -
201C ALA* 3.5 16.8 - - + +
202C PHE* 2.9 32.4 + - - -
266C HIS* 4.8 0.9 + - - -
267C PHE* 5.4 1.4 - - - -
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Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 6.1 0.2 - - + -
136C LEU* 4.5 20.9 - - + -
137C VAL 2.9 8.9 + - - +
138C PHE* 3.6 44.9 - + + -
139C HIS* 3.2 26.9 + - - +
167C LEU* 5.5 2.5 - - + -
168C GLU* 1.3 73.0 - - - +
170C SER* 1.3 59.7 + - - +
171C ILE* 3.8 9.2 - - + +
202C PHE* 3.4 42.2 - + + -
204C VAL* 5.0 10.3 - - + -
231C ILE* 6.5 0.2 - - + -
234C ILE* 5.5 1.8 - - + -
235C VAL* 3.7 33.2 - - + -
238C ILE* 3.9 32.8 - - + -
239C THR* 5.0 2.0 - - + -
252C LEU* 6.5 0.2 - - + -
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C HIS* 3.2 25.6 + - - -
141C PHE* 3.5 32.7 - - - -
168C GLU* 3.5 18.0 + - - +
169C PHE* 1.3 71.4 - - - +
171C ILE* 1.3 63.2 + - - +
172C TYR 3.4 1.4 + - - -
201C ALA* 4.7 3.5 - - - +
202C PHE 3.0 10.3 + - - -
203C MET* 3.3 8.3 - - - +
204C VAL* 2.8 26.2 + - - +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 4.8 2.5 - - + -
13C GLY* 6.1 0.2 - - - -
16C ILE* 3.5 36.3 - - + -
138C PHE* 5.9 1.3 - - + -
139C HIS 2.9 23.5 + - - +
140C SER* 3.7 12.7 - - - +
141C PHE* 2.9 27.9 + - - +
142C GLY 4.5 0.7 + - - -
169C PHE* 3.8 13.5 - - + +
170C SER* 1.3 74.6 - - - +
172C TYR* 1.3 62.8 + - - +
173C PRO* 3.8 1.2 - - - +
204C VAL* 3.5 19.1 - - + +
206C ASN* 3.4 37.5 - - - +
231C ILE* 4.8 2.5 - - + -
501C GTP 3.8 19.7 + - + +
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Residues in contact with TYR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PHE* 3.8 20.2 - + + -
170C SER 3.4 3.2 + - - +
171C ILE* 1.3 73.0 - - - +
173C PRO* 1.3 82.6 - - + +
203C MET* 4.3 15.5 - - + -
204C VAL 2.8 15.8 + - - +
205C ASP* 3.6 31.2 - - + -
206C ASN* 3.1 26.9 + - - +
303C VAL* 5.8 2.2 - - + -
387C ALA* 2.7 48.4 + - + -
388C TRP* 5.1 1.1 - + - -
390C ARG* 3.7 23.4 + - - +
391C LEU* 3.6 35.1 - - + +
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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