Contacts of the strand formed by residues 156 - 159 (chain C) in PDB entry 2NYM
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 THR 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASN 2.8 13.7 + - - +
45C VAL* 3.1 28.9 - - - +
46C GLN* 2.7 32.1 + - - +
114C LEU* 4.1 7.0 - - - +
154C PRO* 3.6 1.1 - - - +
155C LEU* 1.3 88.5 - - + +
157C ALA* 1.3 57.4 + - - +
164C PHE* 3.6 21.6 - - + -
165C CYS 3.1 9.9 - - - -
166C LEU* 3.5 24.0 - - + -
180C ILE* 4.3 1.6 - - + +
198C LEU* 4.5 15.5 - - + -
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 5.1 1.1 - - - -
46C GLN* 2.9 15.9 - - + +
48C VAL* 5.6 2.0 - - + +
81C LEU* 3.7 28.9 - - + -
112C THR* 4.8 2.2 - - + -
114C LEU* 3.9 18.1 - - + +
156C THR* 1.3 79.2 - - - +
158C LEU* 1.3 61.3 + - - +
159C VAL 4.0 0.2 - - - -
163C ILE 3.6 1.0 - - - +
164C PHE* 3.6 4.0 - - - -
165C CYS* 2.7 39.8 + - + +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.3 14.5 - - + +
46C GLN 2.7 10.5 + - - +
47C GLU* 3.4 20.1 - - + +
48C VAL 3.1 23.5 + - - +
157C ALA* 1.3 73.3 - - - +
159C VAL* 1.3 60.5 + - - +
160C ASP 3.4 1.9 + - - -
161C GLY* 3.3 34.1 - - - +
163C ILE 3.2 18.4 - - - +
164C PHE* 3.7 14.1 - - + -
177C LEU* 3.8 22.0 - - + -
181C ARG* 5.2 4.0 - - - +
234C LEU* 3.5 26.5 - - + -
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Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL 3.3 12.8 - - - +
50C CYS* 4.5 9.2 - - + +
52C VAL* 4.0 15.9 - - + -
54C VAL* 5.1 2.9 - - + -
81C LEU* 5.0 9.9 - - + -
157C ALA 4.7 0.2 - - - +
158C LEU* 1.3 70.9 - - - +
160C ASP* 1.3 73.1 + - - +
162C GLN* 3.2 2.3 + - - +
163C ILE* 2.6 48.0 + - + +
165C CYS* 3.8 24.0 - - - -
278C LEU* 3.7 26.5 - - + -
282C LEU* 4.1 9.8 - - + +
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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