Contacts of the strand formed by residues 99 - 104 (chain C) in PDB entry 2CNW
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 ASN 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C LEU* 3.5 20.3 - - - +
96C LYS* 2.6 54.4 + - - +
97C ASP 4.0 0.6 + - - -
98C ARG* 1.3 78.7 - - - +
100C LEU* 1.3 61.9 + - - +
101C TRP* 3.9 11.6 + - - +
127C ARG* 3.9 7.7 - - - +
182C ASP 2.9 25.8 + - - +
183C LEU* 3.6 17.7 - - + -
184C ILE* 2.8 30.9 + - - +
212C ASP* 3.3 5.1 - - - +
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Residues in contact with LEU 100 (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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98C ARG* 5.3 6.1 - - + -
99C ASN* 1.3 73.9 - - - +
101C TRP* 1.3 69.4 + - - +
102C PHE* 3.7 21.8 - - + -
172C VAL* 4.7 7.0 - - + -
173C GLU* 6.2 3.4 - - + -
184C ILE* 3.4 35.9 - - + -
186C VAL* 3.6 22.4 - - + -
209C LEU* 3.8 28.9 - - + +
210C GLY 4.6 2.2 - - - +
211C PRO* 3.3 13.6 - - + +
212C ASP* 2.6 43.7 + - - +
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Residues in contact with TRP 101 (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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93C PRO* 3.8 20.6 - - + -
95C LEU* 3.6 24.9 - - + -
99C ASN* 3.9 16.6 + - + +
100C LEU* 1.3 90.1 - - - +
102C PHE* 1.3 64.2 + - - +
103C LEU* 5.0 2.7 - - + -
118C LEU* 4.1 15.9 - - + -
122C TYR* 3.6 39.7 - + - -
183C LEU* 3.8 11.0 - - + -
184C ILE 2.8 10.3 + - - +
185C LEU* 3.7 24.5 - - + -
186C VAL* 2.7 36.9 + - - +
212C ASP* 4.6 3.2 - - + +
213C GLU* 3.2 36.0 - - + +
215C LEU* 3.9 21.5 - - + -
269C PHE* 4.9 0.2 - + - -
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Residues in contact with PHE 102 (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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100C LEU* 3.7 12.8 - - + -
101C TRP* 1.3 80.9 - - - +
103C LEU* 1.3 63.2 + - - +
104C VAL* 3.9 13.5 - - + -
186C VAL* 3.6 12.8 - - + -
188C THR* 4.5 3.8 - - + -
202C LEU* 4.2 20.2 - - + -
205C LEU* 3.5 36.1 - - + -
206C LYS* 3.4 37.0 - - + -
209C LEU* 3.6 22.9 - - + -
211C PRO* 3.7 17.3 - - + -
213C GLU 2.9 10.6 + - - +
214C VAL* 4.2 10.5 - - + -
215C LEU* 2.8 30.5 + - - +
237C VAL* 5.2 0.9 - - + -
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Residues in contact with LEU 103 (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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101C TRP* 4.7 3.8 - - + +
102C PHE* 1.3 77.0 - - - +
104C VAL* 1.3 56.1 + - - +
111C LYS* 3.5 34.8 - - + +
114C THR* 3.8 19.3 - - + -
115C ALA* 3.7 27.1 - - + +
118C LEU* 4.2 13.7 - - + -
185C LEU* 4.5 10.5 - - + -
186C VAL 2.9 30.1 + - - +
187C ASP* 4.7 2.0 - - - -
188C THR* 2.6 33.4 + - - -
215C LEU* 3.6 9.9 - - + -
217C VAL* 3.9 16.8 - - + -
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Residues in contact with VAL 104 (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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102C PHE* 3.9 13.7 - - + -
103C LEU* 1.3 79.5 - - - +
105C GLY* 1.3 60.1 + - - +
111C LYS* 3.4 9.9 - - - +
188C THR* 3.7 9.2 - - - +
202C LEU* 3.8 33.0 - - + -
214C VAL* 3.9 30.5 - - + -
215C LEU 2.9 15.4 + - - +
216C LEU* 3.6 12.5 - - + +
217C VAL 2.8 25.8 + - - -
233C PHE* 3.9 16.4 - - + -
237C VAL* 5.8 0.4 - - + -
239C VAL* 4.6 3.6 - - + -
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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