Contacts of the helix formed by residues 168 - 180 (chain A) 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 GLY 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 3.0 15.9 + - - -
166A GLY 3.2 0.2 + - - -
167A LYS* 1.3 77.4 - - - +
169A SER* 1.3 62.5 + - - +
170A VAL* 3.3 3.8 + - - -
171A ALA* 3.5 9.4 + - - +
172A ALA* 3.0 26.9 + - - +
200A SER* 4.5 8.0 + - - -
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Residues in contact with SER 169 (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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32A LYS* 2.9 26.5 + - - -
36A THR* 4.6 0.4 + - - -
164A ALA* 3.5 32.1 - - - -
165A ILE* 3.6 12.6 - - - +
166A GLY 2.9 12.3 + - - -
167A LYS 3.4 1.0 + - - -
168A GLY* 1.3 75.3 - - - +
170A VAL* 1.3 57.1 + - - +
172A ALA* 3.8 0.2 - - - +
173A LYS* 2.7 50.1 + - - +
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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
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32A LYS* 4.0 12.8 - - - +
167A LYS 5.3 1.3 - - - +
168A GLY 3.3 0.8 - - - -
169A SER* 1.3 84.0 + - - +
171A ALA* 1.3 61.0 + - - +
173A LYS* 3.5 13.2 + - - +
174A THR* 3.2 24.4 + - - +
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Residues in contact with ALA 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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168A GLY* 3.5 11.0 + - - +
169A SER 3.4 0.2 - - - -
170A VAL* 1.3 77.6 - - - +
172A ALA* 1.3 59.0 + - - +
174A THR* 2.8 24.5 + - - +
175A PHE* 2.9 15.0 + - - +
199A GLU* 6.4 2.2 - - + -
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Residues in contact with ALA 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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36A THR* 4.8 4.3 - - + -
38A LEU* 5.2 0.9 - - + -
164A ALA* 3.7 21.3 - - + -
168A GLY 3.0 20.0 + - - +
171A ALA* 1.3 75.9 - - - +
173A LYS* 1.3 58.4 + - - +
175A PHE* 3.3 4.6 + - - +
176A LEU* 2.9 35.4 + - - +
196A THR* 3.7 23.0 - - + +
199A GLU* 6.6 0.2 - - - -
200A SER* 4.7 10.1 - - - +
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Residues in contact with LYS 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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160A TRP* 4.9 13.5 - - + -
163A THR* 3.4 23.3 - - - +
164A ALA 3.7 20.5 + - - +
169A SER* 2.7 48.2 + - - +
170A VAL* 3.8 12.3 - - - +
172A ALA* 1.3 72.9 - - - +
174A THR* 1.3 61.0 - - - +
176A LEU* 3.3 8.8 + - - +
177A GLU* 3.0 35.1 + - + +
56B SER* 5.8 4.3 - - - +
58B LEU* 3.9 5.4 - - + +
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Residues in contact with THR 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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170A VAL* 3.2 14.3 + - - +
171A ALA* 2.8 12.7 + - - -
173A LYS* 1.3 75.5 - - - +
175A PHE* 1.3 66.4 + - - +
176A LEU 3.2 0.9 + - - -
177A GLU* 3.2 25.0 + - - +
178A LYS* 3.4 33.6 + - - +
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Residues in contact with PHE 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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171A ALA 2.9 12.2 + - - +
172A ALA* 3.8 8.7 - - - +
174A THR* 1.3 78.9 - - - +
176A LEU* 1.3 61.5 + - - +
178A LYS* 3.5 15.1 + - + +
179A ARG* 3.2 56.4 + - + +
192A ILE* 4.3 1.6 - - + -
195A LEU* 3.8 20.6 - - + -
196A THR* 3.3 50.9 - - - -
199A GLU* 5.2 10.8 - - + -
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Residues in contact with LEU 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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38A LEU* 4.7 5.2 - - + -
39A GLY 4.8 1.1 - - - +
40A ILE* 3.7 26.9 - - + -
162A ALA* 4.3 7.2 - - + -
163A THR* 3.8 42.2 - - - +
164A ALA* 4.3 5.4 - - + +
172A ALA 2.9 26.7 + - - +
173A LYS* 3.6 6.1 - - - +
174A THR 3.1 0.2 - - - -
175A PHE* 1.3 74.0 - - - +
177A GLU* 1.3 66.7 + - - +
178A LYS 3.1 1.7 + - - -
179A ARG* 3.2 3.1 + - - +
180A TRP* 3.0 27.9 + - + +
192A ILE* 4.0 7.8 - - + +
196A THR* 3.4 28.3 - - + +
58B LEU* 4.2 9.4 - - + -
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Residues in contact with GLU 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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173A LYS* 3.0 22.7 + - + +
174A THR* 3.2 17.0 + - - +
176A LEU* 1.3 75.8 - - - +
178A LYS* 1.3 63.6 + - + +
179A ARG 3.6 0.2 + - - -
180A TRP* 3.8 11.3 + - - +
56B SER* 4.4 9.6 + - - -
57B THR* 3.0 29.3 + - + +
58B LEU* 3.2 32.9 - - + +
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Residues in contact with LYS 178 (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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174A THR* 3.4 31.3 + - - +
175A PHE* 3.6 21.1 - - + +
176A LEU 3.1 0.6 - - - -
177A GLU* 1.3 81.3 - - + +
179A ARG* 1.3 68.0 + - - +
180A TRP 3.7 1.6 + - - +
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Residues in contact with ARG 179 (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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175A PHE* 3.2 47.7 - - + +
176A LEU 3.2 2.7 + - - +
178A LYS* 1.3 83.4 - - - +
180A TRP* 1.3 61.7 + - - +
181A ASN* 3.6 14.7 + - - -
184A LEU* 4.2 0.2 - - - +
191A HIS* 4.7 8.1 + - - -
192A ILE* 3.6 43.9 - - + +
195A LEU* 3.5 26.7 - - - +
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Residues in contact with TRP 180 (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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40A ILE* 3.9 17.5 - - + -
41A LYS* 3.0 28.6 + - + -
161A LYS* 3.5 55.7 + - + -
162A ALA* 4.1 13.5 - - + -
176A LEU* 3.0 18.7 + - + +
177A GLU 3.8 7.7 + - - +
178A LYS 3.5 2.6 - - - +
179A ARG* 1.3 76.6 - - - +
181A ASN* 1.3 82.3 + - - +
182A ASP* 3.7 24.9 - - + -
184A LEU* 3.5 17.4 - - + +
192A ILE* 5.1 0.9 - - + -
58B LEU* 4.5 17.4 - - + +
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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