Contacts of the helix formed by residues 178 - 186 (chain A) in PDB entry 5TQB
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 ALA 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 2.8 35.9 + - + +
176A ILE* 3.5 5.6 + - + +
177A GLY* 1.3 78.2 - - - +
179A GLY* 1.3 64.8 + - - +
180A PRO 3.5 0.7 - - - -
181A ASP* 3.1 7.3 + - - +
182A VAL* 3.1 27.4 + - + +
209A PRO* 4.7 3.1 - - + -
254A PHE* 4.0 28.7 - - + -
256A VAL* 5.0 4.0 - - + -
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Residues in contact with GLY 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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173A LEU* 3.4 8.5 + - - -
174A LYS* 4.2 21.5 + - - +
177A GLY* 3.1 1.8 - - - -
178A ALA* 1.3 75.1 - - - +
180A PRO* 1.3 66.3 - - - +
182A VAL* 3.0 8.7 + - - +
183A GLU* 2.9 30.5 + - - +
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Residues in contact with PRO 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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142A GLN* 3.9 24.2 - - + +
144A SER* 5.9 1.6 - - - +
145A THR* 3.9 26.0 - - + +
174A LYS 5.9 0.2 - - - +
177A GLY* 3.5 14.1 - - - +
178A ALA 3.7 0.2 - - - -
179A GLY* 1.3 88.1 - - - +
181A ASP* 1.3 55.7 + - - +
183A GLU* 3.9 11.4 - - + +
184A LYS* 3.1 26.2 + - - +
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Residues in contact with ASP 181 (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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141A HIS* 2.9 24.0 + - - -
142A GLN* 3.2 33.5 + - - +
178A ALA 3.1 9.6 + - - +
180A PRO* 1.3 78.0 - - - +
182A VAL* 1.3 64.1 + - - +
183A GLU 3.3 0.2 - - - -
184A LYS* 3.0 40.1 + - - +
185A VAL* 3.5 13.0 - - - +
208A GLY* 3.9 1.2 - - - -
209A PRO* 3.4 16.6 - - + +
254A PHE* 3.3 21.7 - - + -
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Residues in contact with VAL 182 (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 TYR* 4.3 20.2 - - + +
173A LEU* 4.1 14.1 - - + -
178A ALA* 3.1 17.2 + - + +
179A GLY* 3.0 8.4 + - - +
181A ASP* 1.3 78.1 - - - +
183A GLU* 1.3 61.4 + - - +
185A VAL* 3.3 21.9 + - - +
186A LYS* 3.5 5.5 + - - +
209A PRO* 4.1 13.9 - - + -
229A ILE* 4.0 16.4 - - + -
230A PRO* 3.9 21.0 - - + +
231A GLY* 5.9 0.2 - - - -
232A VAL* 4.0 20.6 - - + -
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Residues in contact with GLU 183 (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 TYR* 5.4 5.1 + - - +
179A GLY 2.9 16.5 + - - +
180A PRO* 4.1 9.8 - - - +
182A VAL* 1.3 74.0 - - - +
184A LYS* 1.3 60.8 + - - +
186A LYS* 2.8 46.3 + - + +
187A LYS* 3.6 2.9 + - - +
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Residues in contact with LYS 184 (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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139A ARG 5.5 0.2 + - - -
140A GLY 3.2 30.4 + - - +
141A HIS* 4.0 1.2 + - - +
142A GLN* 4.0 17.7 - - + +
180A PRO 3.1 20.1 + - - +
181A ASP* 3.0 28.8 + - - +
182A VAL 3.3 0.2 - - - -
183A GLU* 1.3 76.4 - - - +
185A VAL* 1.3 62.7 + - - +
187A LYS* 3.2 22.0 + - - +
207A ARG* 2.9 65.0 + - - +
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Residues in contact with VAL 185 (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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181A ASP 3.5 15.7 - - - +
182A VAL* 3.5 9.2 - - - +
183A GLU 3.1 0.8 - - - -
184A LYS* 1.3 75.5 - - - +
186A LYS* 1.3 58.1 + - - +
187A LYS 2.9 22.2 + - - +
188A SER 4.7 3.1 - - - -
205A GLN* 3.7 23.3 - - - +
207A ARG* 3.8 24.5 - - + +
208A GLY* 4.2 14.4 - - - +
230A PRO* 4.5 6.3 - - + +
231A GLY* 3.7 33.0 - - - +
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Residues in contact with LYS 186 (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 TYR* 5.2 12.1 + - - +
182A VAL 3.5 3.8 + - - +
183A GLU* 2.8 33.4 + - + +
185A VAL* 1.3 77.2 - - - +
187A LYS* 1.3 57.7 + - - +
188A SER 3.8 2.7 + - - -
230A PRO* 5.9 10.5 - - + +
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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