Contacts of the helix formed by residues 156 - 168 (chain C) in PDB entry 3RIK
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 LEU 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLU* 4.1 13.5 - - - +
87C ASP* 5.0 4.0 - - - +
90C ALA* 3.8 18.2 - - + -
91C LEU* 3.5 36.6 - - + -
94C LEU* 3.6 21.8 - - + +
151C GLU* 3.3 9.1 + - + +
152C GLU* 3.2 26.0 + - + +
153C ASP 3.7 0.4 + - - -
155C LYS* 1.3 87.8 - - + +
157C LYS* 1.3 68.7 + - + +
158C ILE 3.6 0.2 - - - -
159C PRO* 3.9 2.4 - - - +
160C LEU* 3.3 27.2 + - - +
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Residues in contact with LYS 157 (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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85C MET* 3.6 38.6 - - + +
86C THR 4.6 4.9 - - - +
87C ASP* 3.3 27.0 + - - +
90C ALA* 4.7 5.4 - - + -
121C VAL* 3.9 11.2 - - - -
122C PRO* 2.6 33.2 + - - +
124C ALA 4.4 6.1 + - - +
133C TYR* 5.0 1.0 + - - -
135C TYR* 3.8 3.2 + - - -
152C GLU 3.0 21.3 + - - +
153C ASP* 3.1 27.3 + - - +
156C LEU* 1.3 75.7 - - - +
158C ILE* 1.3 53.5 - - - +
160C LEU* 3.1 4.7 + - - +
161C ILE* 2.8 42.6 + - + +
220C TYR* 3.8 6.7 + - - +
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Residues in contact with ILE 158 (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 LEU* 4.0 13.0 - - + -
153C ASP 2.9 27.4 + - - +
154C THR* 4.5 1.8 - - - +
157C LYS* 1.3 73.1 - - - +
159C PRO* 1.4 61.3 - - + +
161C ILE* 3.3 7.9 + - - +
162C HIS* 2.8 47.5 + - + -
220C TYR* 3.6 37.9 - - + +
223C HIS* 3.6 51.6 - - + +
225C LEU* 4.1 6.7 - - + +
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Residues in contact with PRO 159 (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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94C LEU* 6.3 2.0 - - + -
153C ASP 3.7 3.1 - - - +
154C THR 3.5 20.4 - - - +
155C LYS* 3.5 25.1 - - - +
156C LEU 3.9 2.9 - - - +
158C ILE* 1.4 96.1 - - + +
160C LEU* 1.3 57.5 + - + +
162C HIS* 3.1 10.6 + - + +
163C ARG* 2.9 37.9 + - - +
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Residues in contact with LEU 160 (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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85C MET* 3.8 22.4 - - + +
90C ALA* 3.6 41.5 - - + +
93C ILE* 4.1 27.1 - - + -
94C LEU* 4.0 14.4 - - + -
105C LEU* 4.3 14.2 - - + +
156C LEU 3.3 12.9 + - - +
157C LYS 3.1 4.9 + - - +
159C PRO* 1.3 74.7 - - + +
161C ILE* 1.3 67.8 + - - +
163C ARG* 3.1 35.2 + - - +
164C ALA* 2.9 23.2 + - - +
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Residues in contact with ILE 161 (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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85C MET* 4.2 19.7 - - + -
119C ILE* 4.4 11.9 - - + -
121C VAL* 3.5 33.4 - - + -
157C LYS* 2.8 29.4 + - + +
158C ILE* 3.7 4.0 - - - +
160C LEU* 1.3 72.8 - - - +
162C HIS* 1.3 63.8 + - - +
164C ALA* 3.1 8.7 + - - +
165C LEU* 3.0 25.6 + - + +
174C LEU* 4.0 22.4 - - + -
220C TYR* 4.4 16.4 - - + -
225C LEU* 3.9 25.1 - - + -
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Residues in contact with HIS 162 (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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158C ILE* 2.8 36.7 + - + +
159C PRO* 3.1 11.0 + - + +
161C ILE* 1.3 73.8 - - - +
163C ARG* 1.3 62.3 + - + +
165C LEU* 3.3 9.9 + - + +
166C GLN* 3.3 35.4 + - - +
223C HIS* 2.7 29.3 + - - +
224C LYS* 3.6 13.2 - - + +
225C LEU* 3.4 22.9 - - + +
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Residues in contact with ARG 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 3.9 7.9 - - - +
98C PRO* 4.4 4.6 + - - +
101C GLN* 2.8 43.0 + - - +
102C ASN* 3.1 30.2 + - - +
105C LEU* 3.8 18.2 - - + +
159C PRO* 2.9 24.3 + - - +
160C LEU* 3.1 23.7 + - - +
162C HIS* 1.3 74.5 - - + +
164C ALA* 1.3 65.6 + - - +
166C GLN* 3.3 17.9 + - - +
167C LEU* 3.2 30.7 + - + +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C MET* 5.5 1.3 - - + -
105C LEU* 4.6 6.4 - - + +
109C PHE* 3.7 44.5 - - + +
119C ILE* 4.0 11.9 - - + -
160C LEU 2.9 13.3 + - - +
161C ILE* 3.5 8.7 - - - +
163C ARG* 1.3 75.7 - - - +
165C LEU* 1.3 64.1 + - - +
167C LEU* 3.3 8.1 + - - +
168C ALA* 3.0 24.7 + - - +
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Residues in contact with LEU 165 (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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119C ILE* 4.6 3.1 - - + -
161C ILE* 3.0 29.8 + - + +
162C HIS* 3.7 12.3 - - - +
163C ARG 3.2 0.4 - - - -
164C ALA* 1.3 76.7 - - - +
166C GLN* 1.3 64.8 + - + +
167C LEU 3.4 0.2 + - - -
168C ALA* 3.4 17.6 + - - +
172C VAL* 3.4 46.0 - - + +
174C LEU* 4.8 6.7 - - + -
225C LEU* 4.6 16.4 - - + -
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Residues in contact with GLN 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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162C HIS* 3.3 28.0 + - - +
163C ARG* 3.3 18.6 + - - +
165C LEU* 1.3 77.4 - - + +
167C LEU* 1.3 64.2 + - + +
168C ALA 3.6 2.4 + - - +
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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
----------------------------------------------------------
102C ASN* 4.6 13.5 - - + +
105C LEU* 3.6 36.8 - - + -
106C LYS* 3.9 34.3 - - + +
109C PHE* 4.8 4.9 - - + -
110C SER* 3.4 26.2 - - - +
163C ARG* 3.2 20.3 + - + +
164C ALA* 3.8 4.0 - - - +
165C LEU 3.2 0.4 - - - -
166C GLN* 1.3 79.4 - - + +
168C ALA* 1.3 64.7 + - - +
169C GLN 3.4 2.4 + - - -
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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
----------------------------------------------------------
109C PHE* 3.3 18.2 - - + +
116C TYR 4.9 1.6 - - - +
164C ALA 3.0 15.9 + - - +
165C LEU 3.8 11.4 - - - +
166C GLN 3.3 3.7 - - - +
167C LEU* 1.3 77.5 - - - +
169C GLN* 1.3 64.3 + - - +
170C ARG 3.6 9.6 + - - +
172C VAL* 3.7 28.7 - - + -
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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