Contacts of the helix formed by residues 167 - 177 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ASP* 5.9 0.2 - - - -
164A SER* 2.8 18.6 + - - -
165A GLY 3.3 1.8 + - - -
166A VAL* 1.3 77.2 - - - +
168A GLN* 1.3 62.5 + - - +
169A VAL 3.4 2.5 - - - -
170A VAL* 3.3 6.7 + - - +
171A LEU* 3.0 30.3 + - - +
195A ALA* 4.5 0.8 - - - +
218A LEU* 3.8 24.7 - - - -
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Residues in contact with GLN 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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111A LEU* 4.4 9.7 + - + +
115A TYR* 3.4 22.2 - - - +
133A PRO* 3.2 45.4 + - - +
136A TYR* 3.3 45.9 + - + +
164A SER 4.2 2.0 + - - -
166A VAL* 3.6 12.6 + - + +
167A GLY* 1.3 76.6 - - - +
169A VAL* 1.3 56.6 + - + +
171A LEU* 3.5 8.1 + - - +
172A GLN* 3.0 29.1 + - - +
198A MET* 3.8 19.3 - - + -
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.6 27.1 - - + +
144A VAL* 4.4 6.7 - - + -
159A PHE* 4.0 14.1 - - + -
161A ASP* 3.4 23.5 + - - +
164A SER 5.3 0.8 + - - +
167A GLY 3.4 0.4 - - - -
168A GLN* 1.3 72.6 - - + +
170A VAL* 1.3 60.8 + - - +
172A GLN* 3.2 2.2 + - - +
173A VAL* 2.9 41.1 + - + +
239A PHE* 3.8 44.9 - - + -
401A 5F4 6.3 0.2 - - + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 4.6 10.3 - - + -
161A ASP* 3.8 15.7 - - + +
164A SER* 4.3 5.4 - - - -
167A GLY 3.3 8.2 + - - +
169A VAL* 1.3 76.3 - - - +
171A LEU* 1.3 52.1 + - - +
173A VAL* 3.9 0.7 - - - +
174A ALA* 2.8 37.6 + - - +
182A HIS* 4.0 17.0 - - + +
183A TYR 3.6 22.7 - - - +
184A GLY* 3.6 14.6 - - - -
216A TYR* 3.9 27.8 - - + -
218A LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 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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111A LEU* 3.8 18.8 - - + -
114A VAL* 4.5 1.3 - - + -
166A VAL 5.0 0.2 - - - +
167A GLY 3.0 23.2 + - - +
168A GLN* 3.9 2.5 - - - +
169A VAL 3.3 0.2 - - - -
170A VAL* 1.3 75.0 - - - +
172A GLN* 1.4 57.5 + - - +
174A ALA* 3.9 3.4 - - - +
175A ALA* 3.0 30.3 + - - +
198A MET* 3.9 37.9 - - + +
199A ASP* 4.9 1.1 - - - -
202A PHE* 3.7 37.4 - - + -
216A TYR* 3.6 43.3 - - + +
218A LEU* 4.5 7.4 - - + -
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Residues in contact with GLN 172 (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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107A LEU* 3.8 18.1 - - + +
111A LEU* 3.7 12.1 - - + +
136A TYR* 2.7 29.1 + - - +
141A PHE* 2.9 54.6 + - - -
144A VAL* 3.5 15.3 - - + +
145A ALA* 3.5 21.4 - - - +
148A ILE* 4.1 5.3 - - + +
168A GLN 3.0 17.5 + - - +
169A VAL 3.2 4.2 + - - +
171A LEU* 1.4 75.6 - - - +
173A VAL* 1.3 61.9 + - - +
175A ALA* 3.3 4.5 + - - +
176A ALA* 3.2 21.7 + - - +
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Residues in contact with VAL 173 (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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144A VAL* 4.1 20.4 - - + -
147A MET* 4.5 4.3 - - + -
148A ILE* 4.1 12.8 - - + -
153A MET* 3.6 26.9 - - + -
159A PHE* 3.8 26.7 - - + -
169A VAL* 2.9 22.8 + - + +
170A VAL 4.1 1.1 - - - +
172A GLN* 1.3 75.6 - - - +
174A ALA* 1.4 57.1 + - - +
176A ALA 3.1 1.0 + - - -
177A THR* 2.8 35.0 + - + +
182A HIS* 3.4 24.5 - - + +
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Residues in contact with ALA 174 (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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101A ARG* 3.0 10.6 + - - -
170A VAL 2.8 22.1 + - - +
171A LEU 4.0 3.1 - - - +
173A VAL* 1.4 72.9 - - - +
175A ALA* 1.3 56.7 + - - +
182A HIS* 3.7 28.1 - - + +
202A PHE* 5.5 0.4 - - + -
213A HIS* 4.1 2.9 - - + -
214A ALA* 2.8 41.1 + - - +
216A TYR* 4.0 19.5 - - + -
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Residues in contact with ALA 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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101A ARG* 3.0 31.9 + - - +
102A PRO* 3.8 13.2 - - + +
107A LEU* 3.5 31.6 - - + -
171A LEU 3.0 18.7 + - - +
172A GLN 3.6 3.4 - - - +
173A VAL 3.3 0.2 - - - -
174A ALA* 1.3 76.2 - - - +
176A ALA* 1.3 57.0 + - - +
202A PHE* 4.0 9.9 - - + -
206A MET* 4.3 2.0 - - + -
212A LYS 4.6 0.2 - - - -
213A HIS* 3.9 11.6 - - - +
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Residues in contact with ALA 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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101A ARG* 3.7 10.7 + - - +
107A LEU* 4.9 7.9 - - + -
148A ILE* 3.9 32.8 - - + +
172A GLN 3.2 13.9 + - - +
173A VAL 3.1 2.3 + - - +
175A ALA* 1.3 78.4 - - - +
177A THR* 1.3 60.2 + - - +
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Residues in contact with THR 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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101A ARG* 2.8 26.6 + - - -
148A ILE* 4.0 20.6 - - + +
153A MET* 3.8 35.2 - - + +
173A VAL* 2.8 21.6 + - + +
174A ALA 3.7 0.2 - - - +
176A ALA* 1.3 78.4 - - + +
178A ASN* 1.3 60.9 + - - +
179A CYS* 3.4 10.8 + - - -
182A HIS* 2.9 26.7 + - - -
214A ALA* 3.4 10.9 - - - +
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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