Contacts of the helix formed by residues 114 - 121 (chain B) in PDB entry 6CNB
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 PRO 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B TYR* 4.9 6.5 - - + +
112B LEU 3.9 6.5 - - - +
113B THR* 1.3 88.4 - - - +
115B PRO* 1.3 70.5 - - + +
116B HIS 3.4 0.7 - - - +
117B GLU* 3.4 20.3 + - + +
118B CYS* 2.8 27.0 + - - +
162B ILE* 5.4 4.7 - - + -
174B LEU* 4.5 27.4 - - + +
33L GLU* 4.9 11.4 - - - +
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR 3.4 0.8 - - - -
114B PRO* 1.3 84.4 - - + +
116B HIS* 1.3 60.2 + - - +
118B CYS* 2.7 20.3 + - + +
119B ARG* 2.9 13.5 + - - +
125B TYR* 3.4 40.2 - - + +
156B LEU* 4.0 21.5 - - + -
161B CYS* 5.0 0.2 - - - -
162B ILE* 4.9 4.7 - - + -
163B LEU* 3.8 32.3 - - + -
174B LEU* 4.5 15.3 - - + -
176B GLU* 5.0 3.1 - - + -
186B ILE* 4.4 6.1 - - + +
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PRO* 3.4 1.0 - - - +
115B PRO* 1.3 82.1 - - - +
117B GLU* 1.3 63.6 + - + +
119B ARG* 2.8 43.0 + - + +
120B LEU* 3.3 34.9 - - + +
174B LEU 4.1 6.9 + - - +
175B ASN* 3.0 54.2 + - + +
176B GLU* 4.1 14.5 - - + +
716B ASN* 5.0 6.9 + - - -
719B LYS* 4.3 4.2 + - + +
720B ARG* 3.5 37.8 + - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 3.2 20.6 + - - -
114B PRO* 3.4 21.8 + - + +
115B PRO 3.3 0.4 - - - -
116B HIS* 1.3 86.3 - - + +
118B CYS* 1.3 63.3 + - - +
119B ARG 3.2 0.7 + - - -
120B LEU* 3.3 16.2 + - - +
121B ARG* 3.0 42.2 + - - +
174B LEU 5.1 1.5 + - - +
175B ASN* 6.5 0.4 - - + -
33L GLU* 5.7 2.2 - - - +
53L HIS* 3.4 33.4 + - + +
54L ARG* 5.3 0.3 - - - +
55L ILE* 3.6 20.6 + - + +
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Residues in contact with CYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 4.2 17.9 - - + +
114B PRO 2.8 14.8 + - - +
115B PRO* 2.7 17.3 + - + +
117B GLU* 1.3 81.3 + - - +
119B ARG* 1.3 59.9 + - - +
121B ARG 3.8 2.1 + - - +
123B MET* 3.5 47.2 + - - +
124B THR 3.8 2.0 - - - -
125B TYR* 3.5 35.9 - - + -
186B ILE* 4.6 3.3 - - + +
189B GLY* 4.6 0.3 - - - -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO 2.9 4.9 + - - +
116B HIS* 2.8 36.2 + - - +
118B CYS* 1.3 77.2 - - - +
120B LEU* 1.3 63.8 + - + +
121B ARG 3.4 0.4 + - - -
122B ASP* 3.8 8.5 + - - +
156B LEU* 3.9 11.3 - - - +
176B GLU* 5.7 4.8 - - - +
180B ASP* 5.2 0.2 + - - -
184B TYR* 3.0 37.0 + - - -
186B ILE* 3.5 28.8 - - + +
189B GLY* 3.7 21.4 - - - +
191B GLU* 4.7 9.5 - - + +
460B ARG* 4.3 2.0 - - - +
716B ASN* 5.3 4.8 - - - +
720B ARG* 3.2 47.5 - - - +
721B ILE 5.6 8.9 - - - +
897B LYS* 4.5 3.8 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 3.3 46.9 - - + +
117B GLU* 3.3 9.2 + - - +
119B ARG* 1.3 81.9 - - + +
121B ARG* 1.3 58.6 + - - +
122B ASP 3.3 1.1 - - - -
175B ASN* 6.2 0.2 - - - +
719B LYS 4.9 4.9 - - - +
720B ARG* 4.9 4.7 - - + -
721B ILE* 4.3 21.5 - - + +
883B GLN* 5.9 0.7 - - - +
885B MET* 3.2 50.8 - - + +
895B LEU* 4.3 2.9 - - - +
897B LYS* 3.4 14.9 + - - +
55L ILE* 3.7 25.1 - - + -
57L LEU* 5.7 5.8 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 5.1 2.6 + - - -
117B GLU* 3.0 32.7 + - - +
118B CYS 3.8 1.0 + - - +
119B ARG 3.4 0.6 - - - -
120B LEU* 1.3 75.4 - - - +
122B ASP* 1.3 72.3 + - - +
123B MET* 3.1 45.2 + - + +
887B SER* 4.6 4.7 - - - -
888B VAL* 3.0 17.0 + - - +
889B SER* 3.6 38.2 + - - -
890B ASP* 4.0 5.7 + - - +
892B ASP* 5.7 0.2 + - - -
895B LEU* 4.3 8.6 - - - +
54L ARG* 3.6 37.3 - - - +
55L ILE* 3.5 24.9 - - + -
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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