Contacts of the helix formed by residues 167 - 177 (chain B) in PDB entry 5DTM
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B SER* 2.8 18.8 + - - -
165B GLY 3.3 1.6 + - - -
166B VAL* 1.3 78.1 - - - +
168B GLN* 1.3 61.8 + - - +
169B VAL 3.4 2.5 - - - -
170B VAL* 3.3 6.7 + - - +
171B LEU* 3.0 30.8 + - - +
195B ALA* 4.5 0.2 - - - +
218B LEU* 3.8 25.1 - - - -
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Residues in contact with GLN 168 (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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111B LEU* 4.3 10.4 + - + +
115B TYR* 3.5 22.2 - - - +
133B PRO* 3.2 44.8 + - - +
136B TYR* 3.3 45.2 + - + +
164B SER 4.1 2.6 + - - -
166B VAL* 3.7 13.0 + - + +
167B GLY* 1.3 75.8 - - - +
169B VAL* 1.3 58.0 + - + +
171B LEU* 3.5 8.3 + - - +
172B GLN* 3.0 29.1 + - - +
198B MET* 3.8 19.1 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.6 28.0 - - + +
144B VAL* 4.4 6.7 - - + -
159B PHE* 4.0 13.7 - - + -
161B ASP* 3.4 22.2 + - - +
164B SER 5.3 1.0 + - - +
167B GLY 3.4 0.4 - - - -
168B GLN* 1.3 71.9 - - - +
170B VAL* 1.3 59.4 + - - +
172B GLN* 3.3 2.0 + - - +
173B VAL* 2.9 40.9 + - + +
239B PHE* 3.8 46.4 - - + -
401B 5F4 6.2 0.2 - - + -
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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
----------------------------------------------------------
159B PHE* 4.6 10.5 - - + -
161B ASP* 3.8 15.7 - - + -
164B SER* 4.3 4.7 - - - -
167B GLY 3.3 8.0 + - - +
169B VAL* 1.3 76.4 - - - +
171B LEU* 1.3 52.8 + - - +
173B VAL* 3.8 1.0 - - - +
174B ALA* 2.8 37.4 + - - +
182B HIS* 4.0 16.7 - - + +
183B TYR 3.6 22.0 - - - +
184B GLY* 3.6 15.3 - - - -
216B TYR* 3.8 28.0 - - + -
217B THR 4.6 0.2 - - - +
218B LEU* 3.8 19.3 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.8 18.4 - - + -
114B VAL* 4.5 2.2 - - + -
166B VAL 5.0 0.2 - - - +
167B GLY 3.0 23.0 + - - +
168B GLN* 3.8 3.1 - - - +
170B VAL* 1.3 75.0 - - - +
172B GLN* 1.4 58.2 + - - +
174B ALA* 3.9 2.8 - - - -
175B ALA* 3.0 30.5 + - - +
198B MET* 3.9 37.9 - - + +
199B ASP* 4.9 1.3 - - - -
202B PHE* 3.7 37.1 - - + -
216B TYR* 3.6 42.6 - - + +
218B LEU* 4.5 7.6 - - + -
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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
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107B LEU* 3.8 17.9 - - + +
111B LEU* 3.7 12.5 - - + +
136B TYR* 2.7 29.2 + - - +
141B PHE* 2.9 52.8 + - - -
144B VAL* 3.5 16.4 - - + +
145B ALA* 3.5 21.4 - - - +
148B ILE* 4.1 4.8 - - + +
168B GLN 3.0 17.1 + - - +
169B VAL 3.3 3.8 + - - +
171B LEU* 1.4 75.8 - - - +
173B VAL* 1.3 62.8 + - - +
175B ALA* 3.3 5.0 + - - +
176B ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 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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144B VAL* 4.1 20.0 - - + -
147B MET* 4.4 4.3 - - + -
148B ILE* 4.1 14.4 - - + -
153B MET* 4.4 8.1 - - + -
159B PHE* 3.8 37.2 - - + -
169B VAL* 2.9 23.0 + - + +
170B VAL 4.1 1.3 - - - +
172B GLN* 1.3 74.5 - - - +
174B ALA* 1.3 56.9 + - - +
176B ALA 3.1 0.9 + - - -
177B THR* 2.8 45.0 + - + +
182B HIS* 3.5 22.7 - - + +
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Residues in contact with ALA 174 (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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101B ARG* 3.0 10.9 + - - -
170B VAL 2.8 22.5 + - - +
171B LEU 4.0 3.1 - - - +
173B VAL* 1.3 72.8 - - - +
175B ALA* 1.3 57.5 + - - +
177B THR 3.7 0.2 - - - +
182B HIS* 3.7 26.3 - - + +
202B PHE* 5.4 0.4 - - + -
213B HIS* 4.1 2.7 - - + -
214B ALA* 2.8 42.9 + - - +
216B TYR* 4.0 19.7 - - + -
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Residues in contact with ALA 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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101B ARG* 3.0 31.6 + - - +
102B PRO* 3.8 13.6 - - + +
107B LEU* 3.5 31.4 - - + -
171B LEU 3.0 19.2 + - - +
172B GLN 3.6 3.1 - - - +
173B VAL 3.3 0.2 - - - -
174B ALA* 1.3 75.9 - - - +
176B ALA* 1.3 56.1 + - - +
202B PHE* 4.0 10.5 - - + -
206B MET* 4.2 2.2 - - + -
212B LYS 4.6 0.2 - - - -
213B HIS* 3.9 11.1 - - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.7 10.5 + - - +
102B PRO 6.2 0.2 - - - -
107B LEU* 4.9 7.6 - - + -
148B ILE* 3.9 33.6 - - + +
172B GLN 3.2 14.3 + - - +
173B VAL 3.1 2.3 + - - +
175B ALA* 1.3 78.8 - - - +
177B THR* 1.3 60.0 + - - +
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Residues in contact with THR 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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101B ARG* 2.8 25.8 + - - -
148B ILE* 4.1 21.5 - - + +
153B MET* 4.4 22.2 - - + -
173B VAL* 2.8 30.9 + - + +
176B ALA* 1.3 78.8 - - + +
178B ASN* 1.3 62.4 + - - +
179B CYS* 3.4 13.4 + - - -
182B HIS* 2.8 25.8 + - - -
214B ALA* 3.4 11.3 - - - +
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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