Contacts of the helix formed by residues 158 - 167 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72K LYS 5.7 0.2 - - - +
73K VAL* 4.3 16.6 - - + -
76K TYR* 3.4 30.3 + - + -
93K PHE* 4.0 22.9 - - + -
95K ILE* 4.3 4.0 - - + -
103K LEU* 3.5 45.5 - - + -
107K ALA* 3.5 20.6 - - + -
112K CYS* 2.7 29.9 + - - +
157L THR* 1.3 71.7 - - - +
159L LYS* 1.3 55.4 + - - +
161L ARG* 3.3 3.2 + - + +
162L CYS* 2.9 37.3 + - - -
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Residues in contact with LYS 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 5.3 5.6 - - - +
104K LEU* 4.6 10.3 - - + +
107K ALA* 3.7 15.2 - - + +
108K ASN* 3.2 31.0 + - - +
112K CYS 3.1 17.1 + - - +
157L THR* 4.1 3.6 - - - +
158L LEU* 1.3 75.2 - - - +
160L GLU* 1.3 65.7 + - - +
162L CYS* 3.1 6.6 + - - +
163L LEU* 2.9 39.0 + - + +
184L LEU* 3.6 11.1 - - - +
187L ASP* 3.1 34.6 + - - +
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Residues in contact with GLU 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L TYR* 4.4 9.4 - - + -
157L THR* 3.0 29.0 + - + +
159L LYS* 1.3 77.2 - - - +
161L ARG* 1.3 62.4 + - - +
163L LEU* 3.2 16.7 + - - +
164L GLN* 3.0 39.9 + - - +
167L ARG* 3.2 29.5 + - - -
192L PRO* 4.6 7.2 - - - +
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Residues in contact with ARG 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K TYR* 5.6 1.1 - - + -
92K GLU* 3.4 33.0 + - - +
93K PHE* 2.9 42.6 + - + +
94K PRO* 5.0 2.8 - - - +
95K ILE* 3.7 18.5 - - + +
82L ARG* 4.3 2.0 - - - +
156L TYR* 4.3 18.1 - - + +
157L THR 2.8 20.8 + - - +
158L LEU* 3.5 11.2 - - + +
160L GLU* 1.3 73.1 - - - +
162L CYS* 1.3 61.8 + - - +
164L GLN* 3.1 38.3 + - - +
165L VAL* 3.2 50.2 + - - +
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Residues in contact with CYS 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE* 3.9 12.1 - - - -
100K ALA* 4.3 5.8 - - - +
103K LEU* 3.7 30.3 - - - -
104K LEU* 3.6 43.3 - - + -
107K ALA* 4.5 0.4 - - - -
158L LEU* 2.9 27.5 + - - -
159L LYS 3.6 5.6 - - - +
161L ARG* 1.3 72.8 - - - +
163L LEU* 1.3 67.3 + - - +
165L VAL* 3.1 4.1 + - - +
166L VAL* 2.8 29.8 + - - +
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Residues in contact with LEU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 4.2 22.2 - - + -
159L LYS* 2.9 33.5 + - + +
160L GLU* 3.2 23.8 + - - +
162L CYS* 1.3 76.0 - - - +
164L GLN* 1.3 62.9 + - - +
166L VAL* 4.0 1.2 - - - +
167L ARG* 3.0 47.5 + - - +
184L LEU* 4.6 2.2 - - + +
187L ASP* 4.1 28.0 - - + +
188L LEU* 3.8 38.5 - - + +
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Residues in contact with GLN 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ARG* 3.1 17.7 + - - -
126L ASP* 3.5 32.6 + - - +
156L TYR* 3.3 43.7 - - - -
160L GLU* 3.0 29.9 + - - +
161L ARG* 3.1 29.5 + - - +
162L CYS 3.2 0.4 - - - -
163L LEU* 1.3 76.1 - - - +
165L VAL* 1.3 57.8 + - - +
167L ARG* 3.8 9.7 - - - +
168L SER* 3.1 28.4 + - - -
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Residues in contact with VAL 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ILE* 3.9 36.3 - - + +
96K ALA 5.0 1.1 - - - +
97K PRO* 5.2 1.6 - - + -
100K ALA* 4.3 17.3 - - + -
161L ARG* 3.4 40.6 - - - +
162L CYS* 3.1 8.6 + - - +
164L GLN* 1.3 74.1 - - - +
166L VAL* 1.3 62.7 + - - +
168L SER* 2.5 25.5 + - - +
169L LEU* 3.1 25.1 - - + +
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Residues in contact with VAL 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K ALA* 3.8 24.5 - - + -
101K LEU* 4.1 18.4 - - + -
104K LEU* 4.3 11.4 - - + -
162L CYS 2.8 25.2 + - - +
163L LEU 4.1 2.0 - - - +
165L VAL* 1.3 72.2 - - - +
167L ARG* 1.4 51.8 + - - +
169L LEU* 2.7 30.3 + - + +
170L VAL* 2.8 37.1 + - + +
178L LEU* 3.9 20.4 - - + -
188L LEU* 3.9 14.6 - - + -
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Residues in contact with ARG 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L ASP* 4.7 0.4 + - - -
160L GLU* 3.2 24.7 + - - -
163L LEU* 3.0 38.9 + - - +
164L GLN* 3.8 11.5 - - - +
166L VAL* 1.4 75.0 - - - +
168L SER* 1.3 61.5 + - - +
169L LEU 3.1 1.4 + - - -
170L VAL 3.2 17.5 - - - +
175L TYR* 3.6 25.3 + - - +
187L ASP 2.8 25.9 + - - -
188L LEU* 3.0 28.8 + - + +
190L ASP 3.4 15.5 + - - -
191L HIS* 4.4 15.1 + - - +
192L PRO* 3.6 25.6 - - - +
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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