Contacts of the helix formed by residues 158 - 167 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H LYS 5.7 0.2 - - - +
73H VAL* 4.3 16.2 - - + -
76H TYR* 3.5 30.2 + - + -
93H PHE* 4.1 21.3 - - + -
95H ILE* 4.3 4.0 - - + -
103H LEU* 3.5 41.3 - - + -
107H ALA* 3.4 24.2 - - + -
112H CYS* 2.7 30.9 + - - +
157I THR* 1.3 71.5 - - - +
159I LYS* 1.3 55.1 + - - +
161I ARG* 3.2 3.2 + - + +
162I CYS* 2.9 37.7 + - - -
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Residues in contact with LYS 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ARG* 5.6 4.5 - - - +
104H LEU* 4.6 10.0 - - + +
107H ALA* 3.7 15.2 - - + +
108H ASN* 3.1 31.8 + - - +
112H CYS 3.1 16.5 + - - +
157I THR* 3.2 4.2 - - - +
158I LEU* 1.3 75.4 - - - +
160I GLU* 1.3 64.3 + - - +
162I CYS* 3.1 6.9 + - - +
163I LEU* 3.0 38.9 + - + +
184I LEU* 3.6 12.1 - - - +
187I ASP* 3.2 34.2 + - - +
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Residues in contact with GLU 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I TYR* 4.4 9.2 - - + -
157I THR* 3.0 25.7 + - + +
159I LYS* 1.3 78.9 - - - +
161I ARG* 1.3 64.7 + - - +
163I LEU* 3.2 17.2 + - - +
164I GLN* 3.0 41.9 + - - +
167I ARG* 3.3 28.4 + - - -
192I PRO* 4.6 7.0 - - - +
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Residues in contact with ARG 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H TYR* 5.7 1.1 - - + -
92H GLU* 3.5 30.7 + - - +
93H PHE* 2.9 42.5 + - + +
94H PRO* 4.9 2.8 - - - +
95H ILE* 3.5 18.7 - - + +
82I ARG* 4.3 2.2 - - - +
156I TYR* 4.3 18.5 - - + +
157I THR 2.7 21.2 + - - +
158I LEU* 3.4 11.0 - - + +
160I GLU* 1.3 74.6 - - - +
162I CYS* 1.3 61.1 + - - +
164I GLN* 3.1 34.2 + - - +
165I VAL* 3.2 49.7 + - - +
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Residues in contact with CYS 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ILE* 4.0 9.6 - - - -
100H ALA* 4.2 5.6 - - - +
103H LEU* 3.7 31.0 - - - -
104H LEU* 3.5 43.5 - - + +
107H ALA* 4.5 0.4 - - - -
158I LEU* 2.9 29.5 + - - -
159I LYS 3.6 5.8 - - - +
161I ARG* 1.3 73.0 - - - +
163I LEU* 1.3 61.3 + - - +
165I VAL* 3.1 4.8 + - - +
166I VAL* 2.8 34.3 + - - +
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Residues in contact with LEU 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H LEU* 4.2 22.4 - - + -
159I LYS* 3.0 34.0 + - + +
160I GLU* 3.2 23.8 + - - +
162I CYS* 1.3 76.2 - - - +
164I GLN* 1.3 57.5 + - - +
166I VAL* 4.0 1.2 - - - +
167I ARG* 2.9 53.0 + - - +
184I LEU* 4.6 2.2 - - + +
187I ASP* 4.0 28.3 - - + +
188I LEU* 3.9 37.4 - - + +
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Residues in contact with GLN 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ARG* 3.1 18.2 + - - -
126I ASP* 3.4 33.0 + - - +
156I TYR* 3.4 43.9 - - - -
160I GLU* 3.0 30.1 + - - +
161I ARG* 3.1 29.8 + - - +
162I CYS 3.1 0.2 - - - -
163I LEU* 1.3 76.8 - - - +
165I VAL* 1.3 62.3 + - - +
167I ARG* 3.9 9.5 - - - +
168I SER* 3.1 24.3 + - - -
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Residues in contact with VAL 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ILE* 3.9 38.6 - - + +
96H ALA 4.9 1.1 - - - +
97H PRO* 5.0 1.8 - - + -
100H ALA* 4.1 17.9 - - + -
161I ARG* 3.3 39.0 - - - +
162I CYS* 3.1 8.1 + - - +
164I GLN* 1.3 74.5 - - - +
166I VAL* 1.3 62.9 + - - +
168I SER* 2.5 25.7 + - - +
169I LEU* 3.1 20.3 - - + +
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Residues in contact with VAL 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ALA* 3.8 23.6 - - + -
101H LEU* 3.9 21.1 - - + -
104H LEU* 4.3 12.1 - - + -
162I CYS 2.8 24.4 + - - +
163I LEU* 4.1 2.5 - - - +
165I VAL* 1.3 71.9 - - - +
167I ARG* 1.3 54.4 + - - +
169I LEU* 2.7 30.5 + - + +
170I VAL* 2.8 34.6 + - + +
178I LEU* 3.8 20.0 - - + -
188I LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I ASP* 4.7 0.6 + - - -
160I GLU* 3.3 24.5 + - - -
163I LEU* 2.9 42.7 + - - +
164I GLN* 3.9 10.9 - - - +
166I VAL* 1.3 75.3 - - - +
168I SER* 1.3 61.5 + - - +
169I LEU 3.1 1.4 + - - -
170I VAL* 3.1 17.9 - - - +
175I TYR* 3.7 26.0 + - - +
187I ASP 2.8 26.5 + - - -
188I LEU* 3.0 28.4 + - + +
190I ASP 3.3 15.7 + - - -
191I HIS* 4.4 14.7 + - - +
192I PRO* 3.6 25.8 - - - +
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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