Contacts of the helix formed by residues 168 - 180 (chain P) in PDB entry 3TDD
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 ASN 168 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32P SER 4.5 1.4 + - - -
36P THR* 4.9 1.2 + - - +
166P GLY 3.9 0.4 + - - -
167P ALA* 1.3 78.1 - - - +
169P THR* 1.3 64.0 + - - +
170P SER* 3.2 4.3 - - - +
171P ALA* 3.6 11.5 + - + +
172P ALA* 3.1 21.1 + - - +
200P THR* 3.1 36.8 + - - +
203P ASP* 3.3 28.8 + - - +
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Residues in contact with THR 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P SER* 3.5 21.7 + - - +
165P VAL* 3.5 31.9 - - - +
166P GLY 3.4 21.6 + - - +
167P ALA 3.0 2.8 + - - +
168P ASN* 1.3 74.5 - - - +
170P SER* 1.3 57.0 + - - +
172P ALA* 3.5 1.6 - - - +
173P GLN* 2.6 40.4 + - - +
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Residues in contact with SER 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ASN* 3.2 1.3 - - - -
169P THR* 1.3 79.1 + - - +
171P ALA* 1.3 66.3 + - - +
173P GLN* 3.8 4.7 - - - +
174P THR* 3.0 30.9 + - - -
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Residues in contact with ALA 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ASN* 3.6 16.4 + - + +
170P SER* 1.3 79.0 - - - +
172P ALA* 1.3 63.4 - - - +
174P THR* 3.4 5.2 + - - -
175P LEU* 3.1 31.8 + - + +
200P THR* 4.0 14.4 - - + -
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Residues in contact with ALA 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P THR* 4.9 6.3 - - + -
38P ILE* 4.8 3.6 - - + -
164P SER* 3.4 26.2 - - - +
168P ASN 3.1 16.3 + - - +
169P THR* 3.5 0.7 - - - +
171P ALA* 1.3 79.9 - - - +
173P GLN* 1.3 63.1 + - - +
175P LEU* 3.3 3.8 + - - +
176P LEU* 3.0 28.8 + - - +
196P THR* 3.7 21.4 - - + +
200P THR* 3.8 8.0 - - + +
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Residues in contact with GLN 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P TRP* 4.7 4.2 - - + -
162P ALA 3.3 25.5 + - - -
163P ILE* 3.6 19.6 - - + +
164P SER* 3.1 32.9 + - - +
169P THR* 2.6 20.9 + - - +
170P SER* 3.8 4.9 - - - +
172P ALA* 1.3 71.8 - - - +
174P THR* 1.3 58.3 + - - +
176P LEU* 3.3 6.4 + - - +
177P GLN* 2.9 40.1 + - - +
56Q LEU* 4.4 24.2 - - + -
58Q LEU* 3.9 17.6 - - + +
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Residues in contact with THR 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170P SER* 3.0 19.9 + - - -
171P ALA* 3.8 5.8 - - - -
173P GLN* 1.3 75.4 - - - +
175P LEU* 1.3 67.1 + - + +
177P GLN* 3.4 10.8 + - - +
178P MET* 3.1 40.7 + - + +
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Residues in contact with LEU 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P ALA* 3.1 20.0 + - + +
172P ALA 3.3 4.2 + - - +
174P THR* 1.3 79.7 - - + +
176P LEU* 1.3 62.0 + - - +
178P MET* 3.5 17.7 + - + +
179P ASP* 3.4 29.7 + - - +
192P LEU* 4.5 2.3 - - - +
196P THR* 4.1 19.3 - - + +
199P LYS* 3.9 46.0 - - + +
200P THR* 3.8 23.1 - - + -
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Residues in contact with LEU 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P ILE* 4.3 15.3 - - + -
40P ILE* 3.6 33.7 - - + -
162P ALA* 4.5 10.8 - - + -
163P ILE 4.3 17.7 - - - +
164P SER* 4.5 3.4 - - - -
172P ALA 3.0 22.1 + - - +
173P GLN* 3.6 25.8 - - - +
175P LEU* 1.3 71.6 - - - +
177P GLN* 1.3 59.0 + - - +
178P MET 2.9 5.1 + - - -
180P TYR* 2.9 37.7 + - - +
192P LEU* 3.9 10.8 - - + -
196P THR* 3.6 21.8 - - + +
58Q LEU* 4.4 4.0 - - + -
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Residues in contact with GLN 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P GLN* 2.9 24.2 + - - +
174P THR* 3.8 9.6 - - - +
176P LEU* 1.3 74.7 - - - +
178P MET* 1.3 57.7 + - - +
180P TYR* 4.6 4.5 + - - +
56Q LEU* 6.2 1.2 - - - +
57Q LYS* 3.0 41.2 + - - +
58Q LEU* 3.8 24.4 - - + +
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Residues in contact with MET 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P THR* 3.1 33.8 + - + +
175P LEU* 3.5 19.7 - - + +
176P LEU 2.9 0.6 - - - -
177P GLN* 1.3 81.4 - - - +
179P ASP* 1.3 74.8 - - - +
180P TYR 3.7 1.1 - - - -
199P LYS* 6.3 0.2 - - - -
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Residues in contact with ASP 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P LEU* 3.4 17.0 + - - +
176P LEU 3.3 2.6 + - - -
178P MET* 1.3 99.2 - - - +
180P TYR* 1.3 62.1 + - - +
181P LYS* 3.7 8.1 + - - +
184P MET* 4.6 4.5 - - - +
192P LEU* 4.2 25.2 - - + +
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Residues in contact with TYR 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ILE* 3.9 11.9 - - + -
41P MET* 2.7 31.2 + - - +
161P LYS* 3.4 48.0 - - + +
162P ALA* 4.1 11.7 - - + -
176P LEU 2.9 20.3 + - - +
177P GLN* 4.6 3.1 - - - +
178P MET 3.7 2.0 - - - +
179P ASP* 1.3 79.3 - - - +
181P LYS* 1.3 71.2 + - - +
182P ASP* 3.8 20.1 + - - -
184P MET* 3.6 25.9 - - + +
192P LEU* 4.2 7.9 - - + -
58Q LEU* 4.3 21.3 - - + -
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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