Contacts of the helix formed by residues 160 - 170 (chain C) in PDB entry 3F98
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 TYR 160 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 4.3 5.8 + - - -
149C PHE* 3.3 39.1 - + + -
151C HIS* 3.5 27.1 - - + -
152C GLY* 3.1 16.6 + - - -
155C ALA* 3.8 16.3 - - + +
156C PHE 4.3 3.1 - - - -
157C ARG 4.5 5.2 + - - +
158C THR 3.3 1.0 - - - -
159C LEU* 1.3 85.9 - - + +
161C SER* 1.3 59.7 + - - +
162C ALA 3.3 2.7 - - - -
163C ILE* 3.4 8.1 + - + +
164C GLY* 2.9 23.2 + - - -
272C HIS* 2.7 47.0 + + + -
354C PHE 3.5 17.7 - - - -
355C ALA* 3.7 18.8 - - + +
356C ASP* 3.7 3.4 - - - +
473C NTJ 4.0 3.3 - - - +
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Residues in contact with SER 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.6 4.7 - - - +
84C TYR* 3.4 29.3 + - - -
97C TRP* 4.2 0.3 - - - -
130C THR* 2.6 34.6 + - - -
158C THR 4.0 5.2 - - - -
160C TYR* 1.3 76.5 - - - +
162C ALA* 1.3 61.1 + - - +
164C GLY 4.2 0.2 - - - +
165C ILE* 2.8 40.2 + - - +
356C ASP* 2.6 23.1 + - - -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 4.0 14.6 - - + +
57C PRO* 4.2 16.6 - - + +
58C ARG 6.1 0.2 - - - -
161C SER* 1.3 77.0 + - - +
163C ILE* 1.3 63.5 + - + +
165C ILE* 4.4 0.5 - - - +
166C ASP* 3.2 24.4 + - - +
354C PHE 5.8 1.3 - - - +
355C ALA 6.0 0.2 - - - -
356C ASP* 2.9 17.4 + - - +
359C PHE* 3.7 26.2 - - + -
381C ILE* 4.4 11.0 - - + -
385C ASN* 3.9 4.6 + - - -
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Residues in contact with ILE 163 (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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149C PHE* 4.1 28.7 - - + -
160C TYR* 3.4 10.9 + - + +
161C SER 3.2 0.2 - - - -
162C ALA* 1.3 76.0 - - + +
164C GLY* 1.3 65.3 + - - +
166C ASP* 3.2 3.1 + - - +
167C LEU* 3.0 41.3 + - + +
174C VAL* 6.3 0.2 - - + -
270C ILE* 5.2 3.4 - - + -
295C LEU* 3.7 28.7 - - + -
354C PHE* 3.3 25.4 - - + +
381C ILE* 4.0 17.3 - - + -
384C SER* 5.6 0.7 - - - +
385C ASN* 3.7 22.4 - - - +
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Residues in contact with GLY 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TYR* 3.8 27.7 - - - +
149C PHE* 6.5 0.4 - - - -
160C TYR 2.9 15.1 + - - -
161C SER 3.9 0.2 - - - -
163C ILE* 1.3 77.0 - - - +
165C ILE* 1.3 58.1 + - - +
167C LEU 3.4 0.3 + - - -
168C ALA* 2.9 29.5 + - - +
174C VAL* 3.7 20.5 - - - +
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 5.1 1.1 - - + -
57C PRO 4.6 2.5 - - - +
58C ARG 4.5 2.0 - - - -
59C GLY 3.6 22.9 - - - +
65C VAL* 3.5 20.1 - - + +
84C TYR* 3.8 18.2 - - + -
130C THR* 3.3 28.0 - - + +
131C PRO* 3.7 40.6 - - + +
132C ALA* 4.0 11.7 - - + -
161C SER* 2.8 27.9 + - - +
162C ALA 4.4 0.9 - - - +
164C GLY* 1.3 70.2 - - - -
166C ASP* 1.3 64.5 + - - +
168C ALA 3.3 0.3 + - - -
169C SER* 2.8 22.9 + - - -
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Residues in contact with ASP 166 (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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58C ARG 4.6 0.9 - - - +
59C GLY* 3.5 6.3 - - - -
60C ASN* 2.8 43.3 + - - +
162C ALA 3.2 20.6 + - - +
163C ILE 3.7 2.5 - - - +
165C ILE* 1.3 78.0 - - - +
167C LEU* 1.3 62.0 + - + +
169C SER* 2.7 21.2 + - - -
170C HIS* 2.9 28.2 + - - -
385C ASN* 3.4 37.9 - - - +
386C LYS* 5.9 0.5 - - - +
389C LEU* 4.0 6.2 - - - +
579C FMT 5.1 1.7 - - - +
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Residues in contact with LEU 167 (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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147C VAL* 4.3 10.1 - - + -
149C PHE* 5.6 0.9 - - + -
163C ILE* 3.0 36.1 + - + +
166C ASP* 1.3 80.6 - - + +
168C ALA* 1.3 61.7 + - - +
170C HIS* 3.0 13.5 + - - -
172C PHE* 3.2 32.6 + - + -
174C VAL* 3.6 27.8 - - + -
270C ILE* 4.2 18.2 - - + -
385C ASN* 5.6 3.4 - - + +
388C SER* 5.3 5.8 - - - -
389C LEU* 4.0 17.5 - - + -
392C LEU* 3.8 29.2 - - + -
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Residues in contact with ALA 168 (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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63C TYR* 4.1 1.7 - - - -
65C VAL* 3.6 29.6 - - + -
84C TYR* 3.9 3.8 - - + +
85C TYR* 3.7 16.8 - - - +
86C PRO* 3.6 13.2 - - - +
164C GLY 2.9 18.4 + - - +
167C LEU* 1.3 76.0 - - - +
169C SER* 1.3 57.9 + - - +
171C GLY* 2.9 20.1 + - - -
172C PHE 3.2 20.2 - - - +
174C VAL* 4.3 0.8 - - + +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY* 3.4 19.0 - - - -
60C ASN 3.4 0.5 + - - -
61C GLY* 2.8 25.5 + - - -
62C PRO* 3.1 10.6 - - - +
63C TYR* 3.0 48.8 + - - -
65C VAL* 3.4 6.2 - - - +
165C ILE 2.8 14.0 + - - -
166C ASP 2.7 17.7 + - - -
168C ALA* 1.3 76.6 - - - +
170C HIS* 1.3 55.3 + - - +
171C GLY 3.3 0.7 - - - -
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN* 3.8 10.4 + - + +
61C GLY* 3.3 28.6 + - - -
62C PRO* 4.5 0.2 - - + -
63C TYR* 4.0 0.4 - - - -
166C ASP* 2.9 40.7 + - - +
167C LEU 3.0 10.2 + - - +
169C SER* 1.3 77.4 + - - +
171C GLY* 1.3 59.2 + - - +
172C PHE* 3.7 3.4 - - + -
386C LYS* 6.3 0.9 - - + -
389C LEU* 3.5 34.0 - - + +
400C LYS* 4.6 4.2 + - - -
402C PHE* 3.6 25.6 - + + -
405C TRP* 4.2 12.4 - + - -
572C FMT 3.1 42.7 - - - +
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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