Contacts of the helix formed by residues 116 - 118 (chain C) in PDB entry 5NC5
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 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN 4.5 5.2 - - - +
124B GLN 3.6 14.8 - - - +
125B GLN 3.9 6.1 - - - +
126B GLY* 3.3 37.9 - - - +
127B VAL 5.0 4.9 - - - +
128B SER* 6.4 0.2 - - - -
758B TYR* 5.2 4.0 + - - -
112C GLN* 3.4 14.1 - - - +
113C LEU* 3.8 10.8 - - - +
114C ALA 3.3 3.4 - - - -
115C MET* 1.3 94.8 - - + +
117C LEU* 1.3 62.1 + - + +
118C LEU 3.3 3.0 + - - +
123C GLN* 3.7 15.6 + - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN 5.8 2.7 - - - +
758B TYR* 6.0 1.1 - - - -
761B ASP* 5.7 1.7 - - - +
768B VAL* 4.9 8.4 - - + +
770B LYS* 4.8 16.8 - - - +
60C THR 4.3 3.6 - - - +
64C VAL* 3.6 25.3 - - + +
67C GLN* 5.2 5.8 - - - +
68C ASN* 4.2 11.4 - - - +
113C LEU 3.5 22.9 - - - +
114C ALA* 2.8 15.0 + - - +
116C PRO* 1.3 79.5 - - + +
118C LEU* 1.3 61.3 + - - +
119C PRO* 4.2 3.3 - - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B ASP* 6.1 0.4 - - - -
61C VAL* 4.4 15.0 - - + +
64C VAL* 3.7 24.2 - - + -
65C ILE* 4.3 20.0 - - + -
111C LEU* 5.4 1.1 - - + -
114C ALA 3.6 19.1 - - - +
115C MET* 3.4 33.8 + - + +
116C PRO 3.3 2.9 - - - +
117C LEU* 1.3 81.0 - - - +
119C PRO* 1.3 81.4 - - + +
120C GLN 3.4 0.9 + - - -
122C VAL* 4.0 23.1 - - + -
123C GLN* 3.2 15.7 + - + -
127C VAL* 4.1 7.6 - - + -
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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
------------------------------------------------------------
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