Contacts of the helix formed by residues 160 - 164 (chain A) in PDB entry 3T79
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 SER 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR 3.4 4.9 + - - -
159A VAL* 1.3 73.6 - - - +
161A LEU* 1.3 54.0 + - - +
162A LYS* 3.7 11.3 + - - +
163A ASP* 2.6 54.1 + - - +
164A LEU 3.7 0.9 + - - -
229A GLU 3.7 7.3 + - - -
230A HIS* 3.0 35.7 - - - -
231A ILE* 3.5 9.0 + - - +
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Residues in contact with LEU 161 (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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159A VAL* 5.2 0.7 - - - -
160A SER* 1.3 70.5 + - - +
162A LYS* 1.3 57.0 + - - +
164A LEU* 2.8 49.4 + - + +
202A MET* 6.0 1.1 - - - -
206A TYR* 3.3 42.0 - - + +
209A ARG* 5.1 3.6 - - - +
210A PHE* 5.4 5.6 - - + -
225A LEU* 6.3 0.7 - - + -
231A ILE* 3.1 43.5 + - + +
232A PRO 5.0 2.0 - - - +
233A ILE* 3.7 14.8 - - + +
334A ILE* 3.9 21.9 - - + +
337A VAL* 4.9 11.2 - - + -
338A PHE* 5.0 8.3 - - + -
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Residues in contact with LYS 162 (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 SER* 3.0 5.9 + - - +
161A LEU* 1.3 76.6 - - - +
163A ASP* 1.3 63.6 + - - +
164A LEU 3.8 5.8 - - - +
225A LEU 4.3 11.5 + - - +
226A SER 4.4 2.6 + - - -
228A LEU 2.1 34.5 + - - -
229A GLU* 2.7 39.0 + - - +
231A ILE* 3.0 33.2 - - + +
333A ASP* 5.7 8.2 - - + +
334A ILE* 4.3 23.1 - - + -
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Residues in contact with ASP 163 (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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158A THR 5.2 1.0 - - - +
159A VAL* 5.0 0.7 - - - -
160A SER* 2.6 40.6 + - - +
162A LYS* 1.3 74.9 - - - +
164A LEU* 1.3 62.8 + - - +
165A GLN* 3.4 18.0 + - - +
179A HIS* 3.2 34.6 + - + +
180A SER 5.6 0.5 + - - -
181A SER* 4.0 16.6 + - - +
182A LYS* 5.8 2.9 - - - +
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Residues in contact with LEU 164 (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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159A VAL* 5.5 3.1 - - + +
160A SER 3.7 0.6 + - - -
161A LEU* 2.8 29.5 + - + +
162A LYS 3.8 6.6 - - - +
163A ASP* 1.3 81.4 - - - +
165A GLN* 1.3 63.0 + - - +
166A CYS 4.2 0.7 + - - -
177A LEU* 3.4 52.7 - - + +
178A ALA 3.1 25.4 - - - +
179A HIS* 4.1 8.0 - - + -
185A PHE* 5.5 6.5 - - + -
202A MET* 5.3 8.5 - - - -
233A ILE* 6.5 1.6 - - + -
333A ASP 5.3 3.1 - - - +
337A VAL* 4.3 24.1 - - + +
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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