Contacts of the helix formed by residues 196 - 204 (chain C) in PDB entry 4TRZ
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 PRO 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C SER* 2.9 37.7 - - - +
99C PHE* 5.9 1.1 - - + +
181C GLY 4.7 2.0 - - - +
183C ALA 4.1 9.6 - - - +
185C ALA* 3.9 24.2 - - + +
188C ALA* 5.2 1.8 - - + -
194C LEU* 3.5 10.0 - - + +
195C GLU* 1.3 90.3 - - + +
197C PHE* 1.3 65.3 + - - +
198C PHE* 3.4 1.6 - - + +
199C ASP* 3.0 40.0 + - - +
200C SER* 3.6 2.8 + - - -
408C ARG* 5.7 0.2 - - - +
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Residues in contact with PHE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C MET* 4.3 15.0 - - + -
97C SER 4.6 1.4 + - - -
99C PHE* 4.0 25.4 - + + +
146C VAL* 3.9 29.8 - - + -
148C ILE* 4.7 16.6 - - + -
156C VAL* 4.1 17.3 - - + -
158C ALA* 3.7 23.6 - - + -
159C ASN 5.5 1.7 + - - +
180C LEU* 4.0 31.9 - - + -
181C GLY 4.7 4.8 + - - +
182C LEU* 5.7 1.3 - - + -
195C GLU 3.8 1.5 + - - -
196C PRO* 1.3 70.6 - - - +
198C PHE* 1.3 78.6 + + + +
200C SER* 2.9 19.5 + - - -
201C LEU* 3.1 29.1 + - + -
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Residues in contact with PHE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C GLY 5.2 2.2 + - - -
182C LEU* 4.4 27.3 - - + +
183C ALA 6.1 0.2 - - - +
196C PRO* 3.3 2.8 + - + +
197C PHE* 1.3 86.4 - + + +
199C ASP* 1.3 56.9 - - - +
201C LEU* 2.7 44.8 + - + +
202C VAL* 2.9 41.7 + - + +
207C VAL* 5.1 0.7 - - + -
208C PRO 4.3 3.1 - - - -
209C ASN* 3.8 11.7 - - - -
210C LEU 3.6 29.2 - - - -
211C PHE* 3.9 16.8 - + + -
235C MET* 6.4 1.1 - - + -
237C ILE* 4.0 18.8 - - + -
408C ARG* 3.6 35.0 - - - +
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Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TYR* 5.4 1.8 - - - -
185C ALA* 4.3 10.4 + - - +
195C GLU* 4.0 15.4 - - + +
196C PRO* 3.0 36.2 + - - +
197C PHE 3.0 0.2 - - - -
198C PHE* 1.3 80.1 - - - +
200C SER* 1.3 55.8 + - - +
202C VAL* 3.4 7.9 + - - +
203C LYS* 2.8 30.1 + - - +
408C ARG* 2.6 32.3 + - - -
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Residues in contact with SER 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C VAL* 5.1 2.9 - - - -
158C ALA* 4.2 18.8 - - - +
159C ASN* 5.2 0.7 + - - -
195C GLU* 2.5 29.1 + - - +
196C PRO 3.6 6.1 + - - -
197C PHE* 2.9 14.1 + - - -
199C ASP* 1.3 77.4 - - - +
201C LEU* 1.3 57.8 + - - +
203C LYS* 2.8 4.9 + - - -
204C GLN* 2.6 58.7 + - - +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ILE* 5.6 1.6 - - + -
152C PRO* 4.9 3.8 - - + -
154C VAL* 4.0 18.6 - - + -
156C VAL* 3.9 22.4 - - + +
197C PHE* 3.1 21.8 + - + +
198C PHE* 2.7 28.4 + - + +
200C SER* 1.3 81.0 - - - +
202C VAL* 1.3 63.4 + - + +
205C THR* 2.8 43.1 + - - +
207C VAL* 4.0 13.7 - - + -
237C ILE* 3.9 33.7 - - + -
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 2.9 44.6 + - + +
199C ASP* 3.7 7.9 - - - +
201C LEU* 1.3 79.5 - - + +
203C LYS* 1.3 57.9 + - - +
205C THR 2.9 22.2 - - - +
207C VAL* 3.9 19.3 - - + +
208C PRO 4.8 0.9 - - - +
209C ASN* 3.8 33.2 - - + +
408C ARG* 5.8 0.2 - - - +
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLU* 3.5 31.1 + - - +
199C ASP 2.8 18.9 + - - +
200C SER 2.8 5.2 + - - +
202C VAL* 1.3 80.3 - - - +
204C GLN* 1.3 78.4 + - + +
205C THR 3.2 2.2 + - - +
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Residues in contact with GLN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR 4.9 0.6 - - - +
156C VAL* 3.5 20.4 - - + +
157C ARG* 2.7 45.7 + - - +
195C GLU* 4.8 1.2 + - - -
200C SER* 2.6 34.5 + - - +
203C LYS* 1.3 94.5 - - - +
205C THR* 1.3 61.0 + - - +
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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