Contacts of the helix formed by residues 164 - 182 (chain B) in PDB entry 4TLG
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 TRP 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LYS* 3.5 59.5 - - + +
112B LEU* 3.9 23.3 - - + -
113B LEU* 4.7 6.7 - - + -
160B LEU 4.0 2.0 + - - -
161B LYS* 3.4 16.8 + - - +
162B HIS 3.3 1.6 - - - -
163B LEU* 1.3 73.5 - - - +
165B LYS* 1.3 70.5 + - - +
166B PRO* 3.7 28.4 - - + +
167B ALA* 2.9 35.3 + - + +
168B VAL 3.1 9.4 + - - -
273B GLN* 6.2 0.4 - - - -
274B VAL* 4.2 26.5 - - + -
304B ARG* 5.0 2.2 - - - +
306B GLN* 5.8 2.4 + - - -
350B ASP* 3.4 43.3 + - + +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU 3.1 7.1 + - - -
164B TRP* 1.3 73.6 - - - +
166B PRO* 1.3 73.2 - - + +
168B VAL* 3.2 5.0 + - + +
169B GLU* 3.0 43.9 + - + +
277B GLN 5.9 1.3 - - - -
279B GLU* 5.5 2.0 + - - -
304B ARG* 3.9 30.6 - - - +
306B GLN* 3.6 30.5 - - - +
380B THR* 4.8 6.7 - - + +
382B GLU* 3.0 31.6 + - - +
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Residues in contact with PRO 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.7 13.6 - - + +
117B LYS* 5.7 0.7 - - - +
164B TRP* 3.7 45.1 - - + +
165B LYS* 1.3 95.8 - - + +
167B ALA* 1.3 59.6 + - - +
169B GLU* 3.5 23.9 + - - +
170B VAL* 3.5 11.1 + - - +
274B VAL* 3.9 19.1 - - + -
306B GLN* 5.0 4.7 - - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 3.5 37.6 - - + +
112B LEU* 3.8 10.4 - - + +
162B HIS 4.4 3.1 - - - +
164B TRP* 2.9 28.1 + - + +
166B PRO* 1.3 72.5 - - - +
168B VAL* 1.3 66.1 + - - +
170B VAL* 3.1 19.2 + - - +
171B TYR 3.4 4.5 + - - -
510B 11A 3.7 16.6 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS 3.8 5.8 - - - +
163B LEU* 3.5 36.8 - - - +
164B TRP 3.1 4.3 + - - +
165B LYS* 3.6 8.7 - - + +
167B ALA* 1.3 76.5 - - - +
169B GLU* 1.3 62.6 + - + +
171B TYR* 3.1 4.9 + - - +
172B GLN* 3.0 44.5 + - + +
204B LEU* 3.9 33.7 - - + -
205B VAL* 5.0 4.3 - - + -
304B ARG* 4.1 4.9 - - - +
510B 11A 3.9 11.7 - - + -
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 5.7 1.1 - - - -
165B LYS* 3.0 38.5 + - + +
166B PRO* 3.6 19.7 - - - +
167B ALA 3.2 0.4 - - - -
168B VAL* 1.3 76.2 - - + +
170B VAL* 1.3 55.8 + - - +
172B GLN* 3.8 18.1 - - - +
173B GLN* 2.9 32.5 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 4.1 20.9 - - + -
117B LYS* 3.8 26.9 - - + -
120B MET* 4.5 22.0 - - + -
121B ILE* 3.4 20.9 - - + +
124B ARG* 4.3 16.2 - - - +
166B PRO 3.5 12.8 + - - +
167B ALA* 3.1 10.4 + - - +
169B GLU* 1.3 76.5 - - - +
171B TYR* 1.3 73.1 + - + +
173B GLN* 4.8 0.9 - - - -
174B PHE* 2.9 25.5 + - - +
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 3.1 30.8 + - - -
103B ILE* 3.2 22.0 - - + +
106B LEU* 4.6 4.4 - - + +
120B MET* 6.1 0.4 - - + -
123B LYS* 5.8 0.2 + - - -
124B ARG* 3.3 40.9 + - - +
153B PHE* 5.2 2.0 - + - -
167B ALA 3.4 2.2 + - - -
168B VAL 3.1 7.1 + - - +
170B VAL* 1.3 84.0 - - + +
172B GLN* 1.3 64.7 + - - +
174B PHE* 3.3 19.9 + + + +
175B PHE* 3.0 51.6 + + - -
205B VAL* 4.1 15.5 - - + -
510B 11A 2.9 42.6 - - + +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.0 34.3 + - + +
169B GLU* 3.8 22.0 - - - +
170B VAL 3.3 0.2 - - - -
171B TYR* 1.3 75.6 - - - +
173B GLN* 1.3 63.1 + - - +
175B PHE 3.3 0.5 + - - -
176B SER* 3.1 25.7 + - - -
204B LEU* 2.9 29.3 + - - +
205B VAL* 4.3 5.8 - - + -
208B PHE* 3.5 49.4 - - + +
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LYS* 4.1 14.2 - - - +
121B ILE* 3.8 19.7 - - + +
169B GLU 2.9 17.8 + - - +
170B VAL 3.9 2.7 - - - +
172B GLN* 1.3 77.2 - - - +
174B PHE* 1.3 60.1 + - - +
176B SER* 3.3 8.5 + - - -
177B ILE* 2.9 44.9 + - + +
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 5.9 1.6 - - - -
121B ILE* 3.9 12.6 - - + +
124B ARG* 3.7 37.9 - - + -
125B ILE* 5.3 2.2 - - + -
128B CYS* 4.0 23.6 - - - -
151B MET* 4.5 20.0 - - + -
153B PHE* 5.7 2.0 - + - -
170B VAL 2.9 21.2 + - - +
171B TYR* 3.6 20.9 - + + +
173B GLN* 1.3 73.2 - - - +
175B PHE* 1.3 89.6 + + - +
177B ILE* 3.3 9.6 + - + +
178B LEU* 2.9 52.3 + - + +
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B MET* 6.5 0.2 - - - -
153B PHE* 4.5 13.9 - + - -
171B TYR* 3.0 44.1 + + - +
172B GLN 4.0 2.7 - - - +
173B GLN 3.3 0.2 - - - -
174B PHE* 1.3 94.2 - + - +
176B SER* 1.3 62.3 + - - +
178B LEU* 3.3 19.6 + - + +
179B GLU* 3.0 29.7 + - - +
186B LEU* 6.1 0.2 - - + -
189B LEU* 4.4 16.2 - - + -
205B VAL* 4.1 20.2 - - + -
208B PHE* 3.6 22.4 - - + +
209B MET* 3.6 39.7 - - + -
213B THR* 5.5 1.6 - - + -
510B 11A 4.3 15.7 - - + -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN 3.1 15.0 + - - -
173B GLN* 3.6 12.4 - - - -
174B PHE 3.3 0.2 - - - -
175B PHE* 1.3 76.8 - - - +
177B ILE* 1.3 61.0 + - - +
179B GLU* 3.4 3.7 + - - +
180B ALA* 3.0 25.7 + - - +
208B PHE* 3.3 28.1 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 4.0 25.8 - - + -
121B ILE* 3.5 32.1 - - + -
125B ILE* 4.3 14.8 - - + -
173B GLN* 2.9 41.8 + - + +
174B PHE* 3.7 8.1 - - + +
176B SER* 1.3 73.1 - - - +
178B LEU* 1.3 60.7 + - - +
180B ALA* 4.6 1.6 - - - -
181B ASN* 2.9 55.4 + - + +
182B TYR* 4.8 5.2 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B CYS* 3.8 18.6 - - - -
151B MET* 5.5 0.2 - - + -
174B PHE* 2.9 34.9 + - + +
175B PHE* 3.5 28.5 - - + +
177B ILE* 1.3 77.9 - - - +
179B GLU* 1.3 60.9 + - - +
182B TYR* 2.8 47.4 + - + +
185B THR* 4.5 1.3 - - - +
186B LEU* 4.0 23.8 - - + -
213B THR* 5.5 2.7 - - + -
501B EDO 3.9 14.6 - - - -
505B EDO 3.3 26.5 - - - +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 5.9 0.7 - - - -
55B MET* 3.3 17.8 - - - +
175B PHE* 3.0 21.6 + - + +
176B SER* 3.9 4.0 - - - +
178B LEU* 1.3 80.5 - - + +
180B ALA* 1.3 61.9 + - - +
183B PRO* 3.9 11.4 - - - +
208B PHE 3.8 9.9 - - - +
209B MET* 3.7 3.8 - - - -
210B SER* 2.9 41.0 + - - +
213B THR* 2.6 28.6 + - - +
501B EDO 2.7 27.6 + - - -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TRP* 3.4 19.3 - - - -
45B ARG* 5.2 6.3 - - - +
55B MET* 3.8 16.7 - - + +
59B HIS* 4.3 3.5 - - - +
176B SER 3.0 17.8 + - - +
177B ILE* 4.6 0.9 - - - -
179B GLU* 1.3 77.8 - - - +
181B ASN* 1.3 73.7 + - - +
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TRP* 3.7 2.0 - - - -
58B ARG 5.0 0.2 - - - -
59B HIS* 2.8 43.8 + - + +
62B PHE* 3.4 28.0 - - + +
177B ILE* 2.9 39.7 + - + +
180B ALA* 1.3 87.8 - - - +
182B TYR* 1.3 70.3 + - + +
183B PRO* 3.3 6.9 - - - +
508B EDO 2.6 31.9 + - - -
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B HIS* 5.1 0.7 - + - -
62B PHE* 5.9 0.9 - + - -
68B LEU* 3.8 9.9 - - + +
125B ILE* 3.6 19.2 - - + +
128B CYS* 3.7 35.0 - - + -
129B GLU* 2.7 37.3 + - - +
132B LEU* 3.6 20.4 - - + -
177B ILE* 4.2 16.6 - - + -
178B LEU* 2.8 23.2 + - + +
181B ASN* 1.3 95.4 - - + +
183B PRO* 1.3 64.4 - - - +
185B THR* 2.7 37.1 + - + +
501B EDO 3.2 9.5 - - - -
505B EDO 4.1 3.6 - - - +
508B EDO 3.6 22.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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