Contacts of the helix formed by residues 164 - 181 (chain A) in PDB entry 1T2E
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 GLY 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A VAL* 5.0 0.2 - - - -
162A GLY 3.6 3.4 + - - -
163A LEU* 1.3 79.6 - - - +
165A GLY* 1.3 63.0 + - - +
166A VAL 3.3 1.7 - - - +
167A LEU* 3.0 9.1 + - - +
168A ASP* 2.8 32.5 + - - +
195A HIS* 3.8 24.7 - - - -
257A MET* 5.4 0.2 - - - -
270A ILE 4.6 1.8 + - - -
271A CYS* 5.0 1.1 - - - +
272A SER* 5.6 2.2 - - - -
336A NAI 4.0 2.5 - - - -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY* 1.3 70.3 - - - +
166A VAL* 1.3 54.5 + - - +
168A ASP* 3.8 7.6 + - - -
169A THR* 2.6 43.5 + - - +
191A ILE* 4.1 9.4 - - - -
270A ILE* 3.3 35.3 + - - +
271A CYS* 4.8 1.8 - - - +
288A GLY* 6.0 1.4 - - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.7 0.4 - - + -
164A GLY 3.2 1.2 + - - +
165A GLY* 1.3 75.2 - - - +
167A LEU* 1.3 58.1 + - - +
169A THR* 3.4 5.2 + - - -
170A SER* 3.1 28.0 + - - -
173A LYS* 5.0 4.6 + - - +
253A ALA* 3.5 28.7 - - + +
256A GLU* 3.8 23.3 - - + +
257A MET* 4.1 20.6 - - + -
269A LEU* 3.7 32.8 - - + -
270A ILE 3.2 17.2 + - - +
338A GOL 5.7 0.7 - - - -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.1 7.1 - - + +
164A GLY 3.0 8.7 + - - +
166A VAL* 1.3 79.1 - - - +
168A ASP* 1.3 65.8 + - - +
170A SER* 2.7 23.7 + - - +
171A ARG* 3.4 39.6 + - - +
195A HIS* 4.2 1.3 - - + -
249A ALA* 3.6 33.9 - - + +
250A PRO* 3.6 20.0 - - + -
253A ALA* 3.9 12.8 - - + +
336A NAI 3.4 39.7 - - + +
337A OXM 3.7 3.6 - - - +
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Residues in contact with ASP 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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164A GLY 2.8 20.8 + - - +
165A GLY* 4.2 3.1 + - - +
167A LEU* 1.3 71.7 - - - +
169A THR* 1.3 64.2 + - - +
171A ARG* 3.2 27.1 + - - +
172A LEU 3.3 8.8 + - - -
191A ILE* 3.7 26.6 - - + +
194A ALA 4.7 0.3 - - - +
195A HIS* 2.6 47.2 + - - -
199A MET* 3.3 25.9 - - - +
232A THR* 3.5 10.5 - - + +
337A OXM 4.4 0.2 - - - +
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 2.6 31.3 + - - +
166A VAL* 3.4 4.0 + - - -
168A ASP* 1.3 73.0 - - - +
170A SER* 1.3 59.9 + - - -
172A LEU* 4.3 1.8 - - - -
173A LYS* 2.8 54.5 + - - +
189A ALA* 3.5 23.1 - - + +
190A HIS* 3.9 1.1 - - - -
191A ILE* 3.3 44.2 - - + +
270A ILE* 4.0 3.4 - - + -
338A GOL 3.4 6.0 + - - +
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 3.1 17.0 + - - -
167A LEU* 2.7 30.4 + - - +
169A THR* 1.3 76.3 - - - +
171A ARG* 1.3 58.3 + - - +
173A LYS* 3.7 11.0 - - - +
174A TYR* 2.7 36.9 + - - +
249A ALA* 4.6 7.5 - - - +
253A ALA* 5.8 0.8 - - - +
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Residues in contact with ARG 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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109A ARG* 4.8 1.2 - - - +
167A LEU* 3.5 41.6 - - - +
168A ASP* 3.4 17.7 + - - +
169A THR 3.0 0.4 - - - -
170A SER* 1.3 78.4 - - - +
172A LEU* 1.3 59.8 + - - +
174A TYR* 3.1 5.1 + - - +
175A TYR* 2.8 55.4 + - + +
232A THR* 4.2 9.0 + - + -
235A THR* 3.2 39.7 - - + +
236A ALA* 4.5 3.4 - - - +
239A ILE* 4.4 3.6 - - - +
246A PRO* 3.6 16.6 - - - +
249A ALA* 5.1 5.1 - - + +
250A PRO* 4.2 3.2 - - - +
337A OXM 2.7 42.0 + - - -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP 3.3 3.8 + - - +
169A THR* 3.2 6.8 + - - +
171A ARG* 1.3 79.6 - - - +
173A LYS* 1.3 64.7 + - - +
175A TYR* 4.0 1.3 - - - -
176A ILE* 3.0 42.7 + - + +
189A ALA* 3.7 25.4 - - + -
190A HIS 5.0 2.0 - - - +
191A ILE* 3.8 23.1 - - + -
201A LEU* 4.2 11.2 - - + -
202A LEU 5.7 0.2 - - - +
206A ILE* 4.1 12.3 - - + -
228A ILE* 3.5 24.5 - - + -
229A PHE* 3.8 16.8 - - + -
232A THR* 3.4 21.6 + - + +
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 5.0 4.9 + - - +
169A THR* 2.8 40.1 + - - +
170A SER* 3.7 7.8 - - - +
172A LEU* 1.3 74.9 - - - +
174A TYR* 1.3 59.6 + - - +
176A ILE* 3.4 0.3 + - - +
177A SER* 2.9 30.7 + - - -
184A PRO* 4.2 7.2 - - + +
185A ARG* 6.0 6.6 - - - +
187A VAL* 3.0 43.7 - - + +
188A ASN* 3.5 24.0 - - - +
189A ALA* 3.7 10.3 - - + +
338A GOL 3.0 30.0 + - - -
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER 2.7 24.5 + - - +
171A ARG* 3.6 5.4 - - - +
173A LYS* 1.3 74.6 - - - +
175A TYR* 1.3 81.3 + + + +
177A SER* 2.7 20.6 + - - -
178A GLN* 3.0 42.3 + - + +
184A PRO* 3.7 35.9 - - + -
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Residues in contact with TYR 175 (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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171A ARG* 2.8 34.6 + - + +
172A LEU 4.1 0.2 - - - +
174A TYR* 1.3 89.3 - + - +
176A ILE* 1.3 64.1 + - - +
178A GLN* 3.3 7.3 + - + +
179A LYS* 3.2 16.6 + - - +
228A ILE* 3.7 33.1 - - + +
231A ARG* 3.7 52.9 + - + -
232A THR* 3.6 21.1 - - - -
235A THR* 2.9 37.2 + - - +
238A GLU* 4.6 1.7 + - - -
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Residues in contact with ILE 176 (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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172A LEU* 3.0 31.9 + - + +
173A LYS 3.8 3.4 - - - +
175A TYR* 1.3 79.2 - - - +
177A SER* 1.3 58.4 + - - +
179A LYS* 3.1 4.6 + - - +
180A LEU* 2.9 49.9 + - + +
187A VAL* 4.1 16.6 - - + -
206A ILE* 3.7 28.0 - - + -
208A VAL* 4.5 0.4 - - + -
210A LEU* 4.3 10.3 - - + -
219A ILE* 4.6 4.0 - - + -
225A LEU* 3.8 28.7 - - + -
228A ILE* 4.1 15.3 - - + -
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Residues in contact with SER 177 (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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173A LYS 2.9 16.0 + - - -
174A TYR 2.7 17.7 + - - -
176A ILE* 1.3 76.6 - - - +
178A GLN* 1.3 72.4 + - - +
181A ASN* 2.8 25.3 + - - -
182A VAL* 3.2 22.5 + - - +
184A PRO* 3.4 30.5 - - - +
187A VAL* 3.7 14.1 - - - +
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Residues in contact with GLN 178 (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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174A TYR* 3.0 53.9 + - + +
175A TYR* 3.8 9.6 - - + +
176A ILE 3.1 0.4 - - - -
177A SER* 1.3 107.9 + - - +
179A LYS* 1.3 62.9 + - - +
181A ASN* 3.3 18.7 - - - +
182A VAL 4.3 4.0 + - - -
184A PRO* 4.0 7.5 - - - +
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Residues in contact with LYS 179 (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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175A TYR 3.2 9.5 + - - +
176A ILE* 3.1 8.0 + - - +
178A GLN* 1.3 82.4 - - - +
180A LEU* 1.3 61.2 + - - +
181A ASN* 3.6 9.0 + - - -
218A LEU 3.3 24.7 - - - +
219A ILE* 3.9 28.5 - - + -
223A GLU* 2.4 34.8 + - - +
228A ILE* 4.7 6.5 - - + -
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Residues in contact with LEU 180 (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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176A ILE* 2.9 29.8 + - + +
177A SER 4.4 0.9 - - - +
179A LYS* 1.3 78.2 - - + +
181A ASN* 1.3 74.3 + - - +
182A VAL* 3.7 18.2 - - + +
208A VAL* 3.6 34.1 - - + -
210A LEU* 4.2 6.1 - - + -
212A PHE* 3.9 20.9 - - + -
218A LEU* 3.6 43.1 - - + +
219A ILE* 4.0 10.5 - - + -
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Residues in contact with ASN 181 (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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177A SER 2.8 11.4 + - - -
178A GLN* 3.3 16.0 - - - +
179A LYS 3.3 10.1 + - - -
180A LEU* 1.3 80.8 + - - +
182A VAL* 1.3 60.8 + - - +
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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