Contacts of the helix formed by residues 158 - 167 (chain C) in PDB entry 1VCB
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 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B VAL* 4.4 13.5 - - + -
76B TYR* 3.5 32.5 + - + -
93B PHE* 3.8 23.6 - - + -
95B ILE* 4.2 4.3 - - + -
103B LEU* 3.3 46.4 - - + -
107B ALA* 3.6 19.7 - - + -
112B CYS* 2.8 27.4 + - - +
157C THR* 1.3 71.7 - - - +
159C LYS* 1.3 58.2 + - - +
161C ARG* 3.2 2.8 + - + +
162C CYS* 2.9 38.0 + - - -
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Residues in contact with LYS 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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104B LEU* 4.5 10.4 - - + +
107B ALA* 3.7 16.7 - - + +
108B ASN* 3.1 32.0 + - - +
112B CYS 3.2 17.8 + - - +
157C THR* 4.0 3.8 - - - +
158C LEU* 1.3 74.8 - - - +
160C GLU* 1.3 64.3 + - - +
162C CYS* 3.0 7.6 + - - +
163C LEU* 2.9 36.5 + - + +
184C LEU* 3.6 11.9 - - - +
187C ASP* 3.2 34.2 + - - +
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Residues in contact with GLU 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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126C ASP* 5.0 0.2 - - - +
156C TYR* 4.4 10.3 - - + -
157C THR* 3.0 26.1 + - + +
159C LYS* 1.3 79.2 - - - +
161C ARG* 1.3 64.0 + - - +
163C LEU* 3.2 17.9 + - - +
164C GLN* 3.0 41.9 + - - +
167C ARG* 3.3 29.0 + - - -
192C PRO* 4.6 7.0 - - - +
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Residues in contact with ARG 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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76B TYR* 5.8 1.3 - - + -
92B GLU* 3.4 39.2 + - - +
93B PHE* 3.0 35.6 + - + +
94B PRO* 5.2 2.2 - - - +
95B ILE* 3.7 18.5 - - + +
82C ARG* 4.3 2.0 - - - +
156C TYR* 4.3 15.0 - - + +
157C THR 2.8 21.2 + - - +
158C LEU* 3.5 10.3 - - + +
159C LYS 3.2 0.2 - - - -
160C GLU* 1.3 73.7 - - - +
162C CYS* 1.3 62.4 + - - +
164C GLN* 3.0 36.0 + - - +
165C VAL* 3.2 49.8 + - - +
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Residues in contact with CYS 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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95B ILE* 3.8 23.3 - - - -
100B ALA* 4.3 6.7 - - - +
103B LEU* 3.8 17.9 - - - -
104B LEU* 3.7 43.3 - - + -
107B ALA* 4.7 0.2 - - - -
158C LEU* 2.9 28.3 + - - -
159C LYS 3.0 6.0 + - - +
161C ARG* 1.3 74.8 - - - +
163C LEU* 1.3 66.2 + - - +
165C VAL* 3.2 4.0 + - - +
166C VAL* 2.9 30.3 + - - +
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Residues in contact with LEU 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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104B LEU* 4.3 21.8 - - + -
159C LYS* 2.9 32.2 + - + +
160C GLU* 3.6 24.2 - - - +
162C CYS* 1.3 75.8 - - - +
164C GLN* 1.3 59.0 + - - +
166C VAL* 4.0 1.2 - - - +
167C ARG* 3.0 52.4 + - - +
184C LEU* 4.6 2.2 - - + +
187C ASP* 4.0 28.5 - - + +
188C LEU* 3.8 37.9 - - + +
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Residues in contact with GLN 164 (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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82C ARG* 3.0 17.7 + - - -
126C ASP* 3.5 32.2 + - - +
156C TYR* 3.4 44.5 - - - -
160C GLU* 3.0 31.3 + - - +
161C ARG* 3.0 29.4 + - - +
163C LEU* 1.3 76.7 - - - +
165C VAL* 1.3 62.3 + - - +
167C ARG* 3.6 10.4 + - - +
168C SER* 3.1 24.1 + - - -
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Residues in contact with VAL 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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95B ILE* 4.1 37.2 - - + +
96B ALA 5.2 1.1 - - - +
97B PRO* 5.3 2.2 - - + -
100B ALA* 4.5 12.3 - - + -
161C ARG* 3.2 41.0 + - - +
162C CYS* 3.2 7.7 + - - +
164C GLN* 1.3 74.7 - - - +
166C VAL* 1.3 63.9 + - - +
168C SER* 2.6 24.6 + - - +
169C LEU* 3.1 30.9 - - + +
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Residues in contact with VAL 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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100B ALA* 4.0 24.0 - - + -
101B LEU* 4.2 19.1 - - + -
104B LEU* 4.4 10.1 - - + -
162C CYS 2.9 25.6 + - - +
163C LEU 4.0 2.5 - - - +
165C VAL* 1.3 73.1 - - - +
167C ARG* 1.3 50.7 + - - +
169C LEU* 2.7 28.3 + - + +
170C VAL* 2.8 38.2 + - + +
178C LEU* 3.8 20.4 - - + -
188C LEU* 3.9 14.4 - - + -
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Residues in contact with ARG 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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126C ASP* 4.6 0.8 + - - -
160C GLU* 3.3 24.4 + - - -
163C LEU* 3.0 43.8 + - - +
164C GLN* 3.9 10.8 - - - +
166C VAL* 1.3 75.7 - - - +
168C SER* 1.3 62.3 + - - +
169C LEU 3.1 0.7 + - - -
170C VAL* 3.2 18.0 - - - +
175C TYR* 3.7 25.2 + - - +
187C ASP 2.9 25.7 + - - -
188C LEU* 3.0 28.1 + - + +
190C ASP 3.4 15.1 + - - -
191C HIS* 4.3 16.4 + - + +
192C PRO* 3.6 26.0 - - - +
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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