Contacts of the helix formed by residues 164 - 173 (chain I) in PDB entry 3D1N
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 THR 164 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A T 3.6 49.1 - - - +
10A A 3.1 9.0 - - - -
158I ARG* 3.5 2.0 - - - +
162I GLY 5.5 1.3 - - - +
163I LEU* 1.3 75.3 - - - +
165I GLN* 1.3 67.0 + - - +
166I THR* 3.8 12.5 + - - +
167I GLN* 2.6 51.5 + - - +
168I VAL* 3.1 12.6 + - - +
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Residues in contact with GLN 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A A 2.7 32.0 + - - +
11A A 2.8 28.3 + - - -
155I LYS* 3.8 0.8 - - - +
158I ARG* 3.2 26.2 - - - +
164I THR* 1.3 71.5 - - - +
166I THR* 1.3 63.6 + - + +
168I VAL* 3.1 3.1 + - - +
169I GLY* 3.0 21.1 + - - -
182I GLN* 3.0 39.1 + - + +
185I ILE* 4.1 18.7 - - + +
186I SER* 3.3 18.6 - - - +
189I GLU* 3.1 18.3 + - - +
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Residues in contact with THR 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A T 5.2 10.8 - - + -
10A A 5.9 1.6 - - - +
164I THR* 3.9 15.0 + - - +
165I GLN* 1.3 75.5 - - + +
167I GLN* 1.3 61.7 + - - +
169I GLY 4.7 0.4 - - - +
170I GLN* 3.3 23.0 + - - +
182I GLN* 3.7 30.2 + - + +
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Residues in contact with GLN 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I GLY 3.8 4.5 + - - +
163I LEU* 3.2 30.1 - - + +
164I THR* 2.6 51.5 + - - +
166I THR* 1.3 75.6 - - - +
168I VAL* 1.3 65.7 + - - +
170I GLN* 3.0 14.6 + - - +
171I ALA* 3.0 21.5 + - - +
224I MSE 4.2 22.4 - - - +
227I VAL* 4.4 13.7 - - + +
232I SER* 5.5 4.0 - - - -
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Residues in contact with VAL 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I PHE* 4.3 11.0 - - + -
158I ARG* 3.3 40.4 - - + -
163I LEU* 4.4 6.1 - - + -
164I THR 3.1 5.2 + - - +
165I GLN* 3.4 7.6 - - - +
167I GLN* 1.3 77.3 - - - +
169I GLY* 1.3 67.5 + - - +
171I ALA* 2.9 18.5 + - - +
172I MSE 3.0 25.8 + - - +
185I ILE* 3.6 23.8 - - + -
208I TRP* 4.0 30.5 - - + -
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Residues in contact with GLY 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I GLN 3.0 10.9 + - - -
166I THR 4.2 1.6 - - - -
168I VAL* 1.3 79.2 - - - +
170I GLN* 1.3 62.5 + - - +
172I MSE 2.8 16.6 + - - +
173I THR* 2.9 15.1 + - - +
180I TYR 3.1 25.5 - - - +
181I SER 4.7 3.4 - - - -
182I GLN 5.0 0.4 - - - -
185I ILE* 4.2 12.5 - - - +
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Residues in contact with GLN 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166I THR 3.3 15.1 + - - +
167I GLN* 3.0 22.8 + - - +
169I GLY* 1.3 73.7 - - - +
171I ALA* 1.3 62.9 + - - +
173I THR* 2.9 31.1 - - - +
174I ALA* 3.3 11.0 - - - +
227I VAL* 3.1 32.4 + - - +
228I GLY* 4.1 0.9 + - - -
229I GLY* 3.1 29.8 + - - -
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Residues in contact with ALA 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I GLN 3.0 12.4 + - - +
168I VAL 2.9 12.9 + - - +
170I GLN* 1.3 84.3 - - - +
172I MSE 1.3 56.5 + - - +
174I ALA* 3.0 20.2 - - - +
208I TRP* 3.4 37.4 + - + +
226I PHE 5.2 1.6 - - - +
227I VAL* 3.9 21.3 - - + +
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Residues in contact with MSE 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I VAL* 3.0 29.6 - - + +
169I GLY* 2.8 9.1 + - - +
171I ALA* 1.3 73.3 - - - +
173I THR* 1.3 56.0 + - - +
174I ALA* 2.6 17.2 + - - +
178I PRO 4.7 0.9 - - - +
180I TYR* 3.5 42.0 - - + -
185I ILE* 4.9 1.1 - - + -
201I LEU* 4.6 0.2 - - + -
204I VAL* 3.7 23.1 - - + -
205I LEU* 3.4 35.4 - - + -
208I TRP* 4.2 33.4 - - + -
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Residues in contact with THR 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I GLY 2.9 21.6 + - - +
170I GLN* 2.9 13.9 - - - +
172I MSE 1.3 70.3 - - - +
174I ALA* 1.3 57.6 + - - +
175I THR 3.7 1.1 - - - -
177I GLY 5.6 2.4 + - - +
178I PRO 3.8 12.2 + - - -
179I ALA* 3.2 20.8 - - + +
180I TYR* 3.0 39.5 - - - +
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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