Contacts of the strand formed by residues 166 - 170 (chain C) in PDB entry 5TIN
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 LEU 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C PRO* 3.8 1.6 - - - +
37C VAL* 3.7 20.9 - - + +
39C VAL* 3.5 31.4 - - + -
94C TRP* 4.0 12.3 - - + -
96C PRO* 4.3 8.1 - - + -
97C ASP* 3.8 10.3 - - - +
158C SER* 3.7 22.9 - - - +
161C TYR* 3.4 27.5 - - + +
162C THR 3.0 13.1 + - - +
163C MET* 3.7 5.9 - - - -
164C ASN 3.9 0.2 - - - -
165C ASP* 1.3 79.1 - - - +
167C ILE* 1.3 67.0 + - - +
168C PHE* 3.7 22.4 - - + -
208C THR* 3.6 12.2 - - - +
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Residues in contact with ILE 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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36C PRO* 3.8 13.7 - - + -
37C VAL 2.9 8.8 + - - +
38C GLN* 3.5 29.0 - - - +
39C VAL* 2.9 29.8 + - - +
163C MET* 3.5 55.2 - - + +
166C LEU* 1.3 78.4 - - - +
168C PHE* 1.3 74.4 + - - +
169C GLU* 3.9 10.3 - - - +
208C THR* 3.7 4.0 - - - +
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Residues in contact with PHE 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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39C VAL* 3.5 27.1 - - + +
41C CYS* 4.5 4.3 - - - -
96C PRO* 4.2 5.8 - - + -
98C LEU* 3.7 40.8 - - + -
156C LEU* 3.6 20.0 - - + -
157C GLU* 3.5 25.1 - - - -
158C SER* 3.6 5.8 - - - -
166C LEU* 3.7 31.6 - - + -
167C ILE* 1.3 82.8 - - - +
169C GLU* 1.3 71.9 + - - +
197C TYR* 4.6 3.1 - - - -
208C THR* 2.9 23.6 + - + +
210C ILE* 3.6 28.9 - - + +
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Residues in contact with GLU 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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38C GLN* 4.2 9.7 - - - +
39C VAL 3.0 11.2 + - - +
40C THR* 3.3 9.0 - - - +
41C CYS* 2.9 25.1 + - - +
167C ILE* 3.9 14.0 - - - +
168C PHE* 1.3 80.4 - - - +
170C TRP* 1.3 70.9 + - - +
197C TYR* 2.2 42.2 + - - -
210C ILE* 3.9 7.4 - - - -
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Residues in contact with TRP 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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40C THR* 4.2 1.3 - - - +
41C CYS 3.4 22.4 - - - -
42C ASN* 4.4 1.6 - - - -
43C ILE* 4.3 19.5 - - + -
156C LEU* 4.0 25.1 - - + -
169C GLU* 1.3 85.4 + - - +
171C GLN* 1.3 70.2 + - - +
172C ASP* 3.7 5.4 + - - +
175C PRO* 3.9 26.2 - - + -
176C VAL* 4.4 5.2 - - + -
195C LEU* 3.8 34.3 - - + +
196C ARG 4.7 3.8 - - - -
197C TYR* 6.0 0.9 - + - -
210C ILE* 3.6 35.0 - - + +
211C GLU 3.1 25.3 + - - +
212C VAL* 3.7 31.6 - - + -
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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