Contacts of the helix formed by residues 86 - 93 (chain B) in PDB entry 5NVL
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 GLU 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B THR* 1.3 76.7 - - - +
87B GLU* 1.3 65.4 + - + +
89B GLN* 3.5 9.6 + - - +
90B ARG* 3.1 23.4 + - - +
208C PRO* 4.4 10.5 - - + +
209C ASN* 4.2 23.2 + - - +
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Residues in contact with GLU 87 (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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140A ARG* 5.5 0.3 + - - -
85B THR* 3.3 7.9 + - - +
86B GLU* 1.3 76.1 - - + +
88B GLU* 1.3 67.2 + - + +
90B ARG* 2.9 38.9 + - - +
91B ASN* 2.9 34.8 + - - +
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Residues in contact with GLU 88 (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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142A GLY 4.7 12.4 - - - +
143A LEU* 5.2 2.0 - - + -
146A ARG* 3.2 32.3 + - - +
83B PRO 3.8 0.7 - - - +
84B PHE* 3.2 16.8 - - + -
85B THR* 2.7 47.3 + - - +
87B GLU* 1.3 74.9 - - + +
89B GLN* 1.3 63.5 + - - +
91B ASN* 4.6 4.7 - - - +
92B PHE* 2.9 45.8 + - + +
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Residues in contact with GLN 89 (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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84B PHE* 3.3 28.0 - - + +
85B THR 3.1 19.1 + - - +
86B GLU* 3.6 11.9 - - - +
88B GLU* 1.3 77.1 - - - +
90B ARG* 1.3 60.7 + - - +
92B PHE* 4.0 1.0 - - - +
93B SER* 2.5 49.5 + - - +
205C ASN 5.3 4.0 + - - +
206C LEU 5.1 1.8 - - - -
207C PRO* 3.6 33.6 - - + +
208C PRO* 4.7 5.6 - - + -
92D PHE 4.0 2.6 + - - -
93D SER* 3.3 29.8 + - - +
94D MET 5.6 0.2 - - - +
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Residues in contact with ARG 90 (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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140A ARG* 4.2 19.0 - - - +
86B GLU 3.1 14.3 + - - +
87B GLU* 2.9 34.8 + - - +
89B GLN* 1.3 77.7 - - - +
91B ASN* 1.3 77.3 + - - +
93B SER* 3.1 4.2 + - - -
94B MET* 2.9 45.3 + - + +
95B SER* 4.8 6.9 + - - -
93D SER* 6.4 0.2 - - - -
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Residues in contact with ASN 91 (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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140A ARG* 3.1 47.5 + - - +
141A LYS 4.9 3.6 + - - -
142A GLY 6.1 0.2 - - - -
143A LEU* 3.8 24.1 - - + +
87B GLU* 2.9 26.3 + - - +
88B GLU* 3.9 1.3 - - - +
90B ARG* 1.3 92.8 + - - +
92B PHE* 1.3 63.0 + - - +
93B SER 3.0 0.2 + - - -
95B SER* 3.0 40.9 + - - +
96B VAL* 3.3 3.4 - - - +
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Residues in contact with PHE 92 (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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142A GLY 5.2 0.7 - - - -
143A LEU* 3.6 42.2 - - + -
146A ARG* 4.0 31.9 - - + -
147A CYS* 3.7 24.9 - - - -
150A ASN* 6.2 1.6 - - - -
204A LEU 4.5 13.7 - - - -
205A ASN* 3.5 15.8 - - + +
206A LEU* 6.1 1.3 - - + -
207A PRO* 3.2 21.9 - - - +
84B PHE* 4.0 24.7 - + + -
88B GLU* 2.9 40.5 + - + +
89B GLN 4.4 1.3 - - - +
91B ASN* 1.3 76.0 - - - +
93B SER* 1.3 57.7 + - - +
96B VAL* 3.8 13.0 - - + -
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Residues in contact with SER 93 (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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207A PRO* 3.8 7.3 - - - +
208A PRO* 5.2 0.2 - - - +
89B GLN* 2.5 43.7 + - - -
90B ARG* 3.6 4.5 - - - -
91B ASN 3.0 0.8 - - - -
92B PHE* 1.3 79.6 - - - +
94B MET* 1.3 64.0 + - - +
89D GLN* 3.2 22.3 + - - +
93D SER* 3.3 26.6 + - - -
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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