Contacts of the helix formed by residues 176 - 181 (chain A) in PDB entry 3RTC
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 LYS 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.2 25.1 - - + +
119A THR* 4.1 15.0 - - + -
147A ASP* 3.4 21.2 + - - -
148A VAL* 4.1 9.6 - - + -
154A SER* 3.7 20.4 - - - +
171A THR* 2.9 14.9 + - - +
172A PHE* 2.9 17.8 + - - +
174A VAL* 2.8 25.5 + - + +
175A PRO* 1.3 76.3 - - - +
177A ILE* 1.3 67.1 + - - +
178A GLY 4.2 1.8 - - - +
179A HIS* 2.9 44.2 + - + +
180A ILE* 3.6 8.3 - - - +
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Residues in contact with ILE 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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154A SER 3.3 4.7 + - - +
155A ASN* 3.3 23.6 - - - +
156A THR 4.4 0.4 - - - +
176A LYS* 1.3 73.7 - - - +
178A GLY* 1.3 56.9 + - - +
180A ILE* 2.9 25.0 + - + +
181A LEU* 3.0 42.3 + - + +
208A ARG* 4.0 23.3 - - + +
385A TYR* 3.3 36.6 - - + +
416A PHE* 4.3 18.4 - - + -
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Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 6.3 0.9 - - - -
152A ILE* 3.6 8.5 - - - +
153A ASP 3.8 4.7 - - - -
154A SER* 2.9 18.9 + - - -
157A GLY* 3.4 26.0 - - - -
176A LYS* 3.1 1.2 + - - +
177A ILE* 1.3 73.9 - - - +
179A HIS* 1.3 60.4 + - - +
181A LEU 3.7 1.2 - - - +
184A GLY* 3.2 30.1 - - - +
185A ARG 3.6 0.2 + - - -
188A THR* 4.3 0.7 + - - -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP 2.7 28.5 + - - -
148A VAL* 3.5 9.7 - - + +
149A PRO* 4.4 4.3 - - + -
152A ILE* 6.3 0.2 - - + -
169A THR* 3.7 7.3 - - + +
171A THR* 3.2 25.6 - - + -
175A PRO* 3.9 4.6 - - + +
176A LYS* 2.9 41.1 + - + +
178A GLY* 1.3 77.4 - - - +
180A ILE* 1.3 62.1 + - + +
185A ARG* 3.2 26.3 - - - +
188A THR* 3.5 26.9 + - + +
191A LEU* 3.8 28.5 - - + +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 4.2 13.9 - - + +
176A LYS 3.6 21.1 - - - +
177A ILE* 2.9 10.5 + - + +
179A HIS* 1.3 84.5 - - + +
181A LEU* 1.3 58.7 + - + +
185A ARG* 3.3 12.5 - - - +
191A LEU* 6.0 0.7 - - + -
208A ARG 5.9 1.6 - - - +
209A TYR 5.5 0.4 - - - -
210A VAL* 3.5 29.4 - - + +
405A THR* 2.7 36.2 + - + +
416A PHE* 3.5 47.1 - - + -
418A ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 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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156A THR* 3.6 21.5 - - - +
157A GLY* 4.1 2.6 - - - -
177A ILE* 3.0 36.0 + - + +
178A GLY 3.7 3.1 - - - +
180A ILE* 1.3 77.8 - - + +
182A PHE* 1.3 62.6 + - - +
184A GLY* 3.1 7.8 + - - -
185A ARG* 2.8 20.3 + - - -
383A TYR* 3.6 47.6 - - + +
385A TYR* 3.8 12.6 - - + -
405A THR* 3.8 21.5 - - + -
407A ILE* 4.6 4.9 - - + -
416A PHE* 4.1 16.6 - - + -
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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