Contacts of the strand formed by residues 163 - 168 (chain G) in PDB entry 3TKR
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 ARG 163 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G PHE 3.9 0.2 - - - -
80G PRO* 3.4 19.7 - - + +
84G THR* 5.4 0.8 + - - -
85G PHE 5.8 0.2 - - - +
86G VAL* 3.4 22.7 - - - +
87G CYS* 3.2 35.4 - - - +
90G GLU* 2.8 37.4 + - - -
162G LEU* 1.3 77.6 - - - +
164G GLY* 1.3 57.3 - - - +
178G THR 3.4 4.3 - - - +
180G ASN* 2.8 44.9 + - + +
181G ASP 4.1 3.1 - - - +
182G LEU* 2.7 32.3 + - - +
184G VAL 3.5 21.1 - - - -
186G ARG* 3.3 26.6 + - - +
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Residues in contact with GLY 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G PHE* 3.4 0.9 - - - -
78G PHE* 2.8 37.2 + - - +
153G VAL* 4.1 10.8 - - - -
162G LEU* 3.3 8.1 + - - +
163G ARG* 1.3 73.7 - - - +
165G LEU* 1.3 59.1 + - - -
166G PHE* 3.8 5.8 - - - -
178G THR 3.3 5.4 - - - -
179G LEU* 3.6 17.7 - - - -
186G ARG* 3.0 6.0 + - - +
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G VAL* 3.8 15.7 - - + -
76G PHE 3.8 3.1 - - - -
77G PHE* 3.8 15.9 - - + -
94G PHE* 3.7 31.0 - - + -
164G GLY* 1.3 74.4 - - - +
166G PHE* 1.3 68.7 + - - +
167G ILE* 3.9 26.5 - - + -
176G GLN* 4.3 8.7 - - - +
177G ILE* 3.5 4.5 - - - +
178G THR* 2.7 44.4 + - - +
186G ARG* 3.9 21.1 - - + +
191G THR* 3.7 15.7 - - + +
194G LEU* 6.1 0.7 - - + -
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Residues in contact with PHE 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ALA* 4.1 7.4 - - + -
74G LEU 3.6 1.2 - - - +
75G VAL* 3.5 3.5 - - - -
76G PHE* 2.8 49.0 + + + +
78G PHE* 3.6 30.7 - + - -
151G TYR* 3.4 50.5 - + + -
153G VAL* 3.5 17.5 - - + -
164G GLY 3.8 8.5 - - - -
165G LEU* 1.3 78.1 - - - +
167G ILE* 1.3 63.2 + - - +
168G ILE* 4.0 2.7 - - + -
174G LEU* 3.8 17.7 - - + -
176G GLN 3.4 3.6 - - - -
177G ILE* 3.8 33.7 - - + -
179G LEU* 4.3 8.5 - - + -
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Residues in contact with ILE 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G TYR* 4.0 27.1 - - + -
74G LEU 3.6 5.2 - - - +
75G VAL* 4.6 9.6 - - + -
165G LEU* 3.9 16.2 - - + -
166G PHE* 1.3 76.1 - - - +
168G ILE* 1.3 62.5 + - - +
174G LEU* 3.5 3.2 - - - +
175G ARG* 2.8 33.0 + - + +
176G GLN* 3.0 36.0 + - + +
191G THR* 4.2 12.3 - - + +
194G LEU* 3.6 33.7 - - + -
195G VAL* 4.2 14.6 - - + +
198G PHE* 4.9 4.0 - - + -
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Residues in contact with ILE 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ALA* 3.7 25.8 - - + -
66G LEU* 4.1 21.3 - - + -
73G TYR* 3.4 6.7 - - - -
74G LEU* 2.7 48.3 + - + +
76G PHE* 4.0 26.9 - - + -
151G TYR* 4.0 13.5 - - + +
166G PHE* 4.5 2.7 - - + +
167G ILE* 1.3 80.1 - - - +
169G ASP* 1.3 70.0 + - - +
172G GLY* 3.7 26.0 - - - +
173G ILE 3.5 4.5 - - - +
174G LEU* 4.1 9.0 - - + -
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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