Contacts of the strand formed by residues 163 - 171 (chain A) in PDB entry 1TPY
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 VAL 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS 4.1 7.0 - - - +
60A LEU* 3.8 22.3 - - + +
132A ARG* 3.6 32.3 - - - +
133A ILE 3.3 21.1 + - - -
158A LEU* 3.8 8.1 - - - +
161A ASP 4.0 6.7 - - - +
162A GLY* 1.3 80.5 - - - +
164A LEU* 1.3 65.2 + - - +
284A THR* 4.1 24.5 - - + -
285A LEU 3.4 12.1 - - - +
286A ALA* 4.5 11.0 - - + -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.1 2.0 - - - -
133A ILE* 3.5 31.9 - - + +
135A SER* 5.0 3.1 - - - -
150A PHE* 4.3 18.2 - - + -
151A PHE* 4.1 20.0 - - + -
154A ALA* 4.3 4.5 - - + -
158A LEU* 4.3 6.3 - - + -
163A VAL* 1.3 75.9 - - - +
165A LEU* 1.3 71.1 + - - +
166A LEU* 4.2 8.7 - - + +
220A PHE* 4.2 18.8 - - + -
283A PHE 3.3 1.9 - - - +
284A THR* 3.8 1.0 - - - -
285A LEU* 2.7 71.8 + - + +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.6 37.9 - - + +
59A LYS* 3.8 18.8 - - + -
60A LEU* 3.6 22.8 - - + +
133A ILE 2.9 11.3 + - - +
134A VAL* 3.6 7.2 - - + -
135A SER 3.0 23.6 + - - +
163A VAL* 5.8 0.2 - - + -
164A LEU* 1.3 74.9 - - - +
166A LEU* 1.3 58.4 + - - +
167A HIS* 3.8 22.7 - - + +
282A GLN* 4.4 11.7 - - + +
283A PHE 3.7 14.4 - - - +
284A THR* 3.7 19.7 - - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 3.8 9.2 - - - +
139A PHE* 3.8 27.6 - - + -
150A PHE* 4.7 9.6 - - + -
151A PHE* 3.7 32.5 - - + -
164A LEU* 3.6 8.0 + - + -
165A LEU* 1.3 71.9 - - - +
167A HIS* 1.3 62.3 + - - +
168A THR* 3.6 27.4 - - + -
211A VAL* 3.8 20.0 - - + -
283A PHE* 2.7 50.6 + - + +
285A LEU* 4.2 10.8 - - + -
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Residues in contact with HIS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A CYS 3.9 19.1 - - - -
52A LYS* 4.1 9.0 - - + +
135A SER 2.8 18.5 + - - +
136A ILE* 3.5 33.2 - - + +
137A GLY 2.9 23.0 + - - -
138A ALA 4.6 0.9 + - - -
139A PHE* 5.0 0.2 - - - +
165A LEU* 3.7 11.4 + - + -
166A LEU* 1.3 73.0 - - - +
168A THR* 1.3 66.2 + - - +
228A LEU* 4.1 12.1 - - + -
280A VAL* 3.6 12.5 - - + +
281A ASN 3.3 4.9 - - - -
282A GLN* 3.3 26.4 + - + +
902A CO3 2.8 37.6 + - - -
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 3.7 20.6 - - + +
140A GLU* 3.1 16.7 + - - +
166A LEU* 3.6 23.6 - - + -
167A HIS* 1.3 77.5 - - - +
169A ILE* 1.3 82.9 + - - +
170A THR* 3.8 2.0 - - + +
206A PRO* 3.8 10.1 - - + +
211A VAL* 4.6 0.2 - - + -
280A VAL* 4.2 2.2 - - - -
281A ASN* 2.9 32.7 + - - +
283A PHE* 4.0 21.3 - - + -
902A CO3 3.5 9.9 - - - -
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 2.9 22.1 + - + +
168A THR* 1.3 88.0 + - - +
170A THR* 1.3 64.6 + - - +
205A PRO* 4.0 13.3 - - + +
206A PRO* 3.3 15.8 - - - +
232A TYR* 3.8 13.2 - - + -
273A PHE* 4.3 2.0 - - + -
278A ILE* 3.2 30.5 - - + -
279A ASP 3.3 5.4 - - - +
280A VAL* 4.0 2.2 - - + +
902A CO3 3.4 26.2 - - - +
1901A 16A 3.7 51.4 - - + -
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 3.6 13.4 + - + +
169A ILE* 1.3 83.1 - - - +
171A GLY* 1.3 61.5 + - - +
206A PRO* 3.2 15.0 - - + +
208A ILE* 3.8 22.3 - - + +
211A VAL* 4.9 0.2 - - + -
278A ILE* 3.6 1.6 - - - +
279A ASP* 2.8 42.7 + - - +
281A ASN* 2.9 25.1 + - - +
283A PHE* 3.9 26.5 - - + -
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A THR* 1.3 76.1 - - - +
172A LEU* 1.3 67.5 + - - -
176A GLN* 4.3 0.5 - - - +
205A PRO* 4.6 10.0 - - - +
206A PRO 2.9 11.4 + - - -
207A THR* 3.3 23.9 + - - -
208A ILE* 4.2 3.3 + - - +
277A TYR 4.4 0.2 - - - -
278A ILE* 4.1 19.1 - - - -
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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