Contacts of the strand formed by residues 143 - 151 (chain F) in PDB entry 6KTR
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 ALA 143 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F PRO* 3.2 25.5 - - - +
142F ALA* 1.3 75.1 - - - +
144F LEU* 1.3 61.3 + - - +
187F VAL* 4.2 14.8 - - + -
188F VAL 4.2 3.8 - - - -
189F THR* 4.8 6.7 - - + +
120G THR* 4.2 30.5 - - + +
122G PHE* 3.4 8.9 - - + -
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Residues in contact with LEU 144 (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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130F LEU 3.5 13.0 - - - +
132F PRO* 3.9 13.0 - - + -
143F ALA* 1.3 74.1 - - - +
145F GLY* 1.3 58.9 + - - +
160F TRP* 3.7 10.5 - - + -
187F VAL* 3.2 5.4 - - - +
188F VAL* 2.9 50.4 + - + +
190F VAL* 3.7 23.1 - - + -
195F LEU* 3.9 14.8 - - + -
200F TYR* 3.5 32.5 - - + -
217F ALA* 3.6 26.7 - - + +
122G PHE* 4.2 2.5 - - - -
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Residues in contact with GLY 145 (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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130F LEU* 2.8 39.9 + - - +
144F LEU* 1.3 75.9 - - - +
146F CYS* 1.3 61.9 + - - -
160F TRP* 3.6 9.9 - - - -
186F SER 3.0 14.1 - - - -
187F VAL* 3.9 5.4 - - - -
217F ALA* 3.6 12.6 - - - +
122G PHE* 4.6 0.4 - - - -
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Residues in contact with CYS 146 (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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127F VAL* 4.4 8.5 - - + -
128F PHE 3.4 7.2 - - - +
129F PRO* 4.7 5.6 - - - -
130F LEU* 4.0 5.9 - - - +
145F GLY* 1.3 78.8 - - - -
147F LEU* 1.3 59.7 + - - +
148F VAL* 3.9 8.0 + - + +
158F VAL* 5.5 0.4 - - + -
160F TRP* 3.7 11.0 - - + -
185F SER* 3.4 6.1 - - - -
186F SER* 2.9 31.7 + - - +
202F CYS* 2.0 54.7 - - + -
204F VAL* 5.3 0.2 - - + -
215F LYS* 4.3 7.4 - - - -
217F ALA* 5.0 2.5 - - - -
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Residues in contact with LEU 147 (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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126F SER 3.4 2.3 - - - +
127F VAL* 3.2 7.1 - - - +
128F PHE* 2.6 64.1 + - + +
130F LEU* 4.1 16.3 - - + +
146F CYS* 1.3 71.9 - - - +
148F VAL* 1.3 64.8 + - - +
149F LYS* 4.2 17.9 - - + -
183F SER* 5.2 2.0 - - - -
184F LEU 3.5 17.3 - - - +
185F SER* 3.8 12.1 - - - +
128G GLU* 4.2 6.5 - - - +
135G THR* 3.9 30.3 - - + +
137G VAL* 4.3 7.9 - - + -
181G TYR* 3.9 18.4 - - + -
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Residues in contact with VAL 148 (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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125F PRO* 3.5 25.6 - - + -
126F SER 3.9 2.0 - - - -
127F VAL* 4.5 2.0 - - + +
146F CYS* 4.2 10.8 - - + +
147F LEU* 1.3 76.0 - - - +
149F LYS* 1.3 58.6 + - - +
151F TYR* 3.6 15.1 - - + -
156F VAL* 4.3 5.8 - - + -
158F VAL* 4.4 4.7 - - + -
183F SER* 3.4 3.6 - - - -
184F LEU* 2.8 62.9 + - + +
186F SER 5.5 0.4 - - - +
204F VAL* 3.7 39.0 - - + -
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Residues in contact with LYS 149 (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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125F PRO* 3.4 1.4 - - - +
126F SER* 2.9 38.0 + - - +
128F PHE* 3.7 13.0 - - + -
147F LEU* 4.2 17.9 - - + -
148F VAL* 1.3 73.8 - - - +
150F ASP* 1.3 92.1 - - - +
151F TYR* 3.7 1.6 - - - -
177F GLN* 5.1 3.1 - - - +
183F SER* 3.4 17.5 - - - +
128G GLU* 2.6 27.0 + - - +
133G LYS* 3.3 37.5 - - - +
134G ALA 4.7 0.2 - - - +
135G THR* 3.4 20.8 + - + +
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Residues in contact with ASP 150 (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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123F LYS* 3.7 19.2 - - - +
124F GLY 3.1 16.1 - - - +
126F SER* 4.5 0.6 + - - +
149F LYS* 1.3 104.3 - - - +
151F TYR* 1.3 57.7 + - - +
177F GLN* 3.1 22.2 + - - +
179F SER* 4.2 3.5 + - - -
181F LEU* 3.8 29.5 - - + +
182F TYR 3.1 13.3 + - - -
183F SER* 3.4 2.4 + - - -
133G LYS* 4.2 12.5 + - - +
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Residues in contact with TYR 151 (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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123F LYS* 3.4 14.1 - - - +
125F PRO* 3.7 29.6 - - + -
148F VAL* 3.6 31.4 - - + -
150F ASP* 1.3 77.4 - - - +
152F PHE* 1.3 63.5 + - - +
153F PRO 3.8 17.5 - - - -
154F GLU* 3.1 26.7 + - + -
156F VAL* 3.5 25.5 - - + +
174F ALA* 3.2 17.3 - - - +
181F LEU* 3.6 3.0 - - - +
182F TYR* 2.9 56.7 + - + -
183F SER* 4.0 1.1 - - - -
184F LEU* 3.5 14.4 - - + +
206F HIS* 3.9 2.7 - - - +
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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