Contacts of the strand formed by residues 135 - 139 (chain C) in PDB entry 2CAN
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 LYS 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C THR* 3.6 9.4 - - - +
133C TYR* 4.3 0.7 - - - +
134C HIS* 1.3 84.4 + - - +
136C VAL* 1.3 65.1 + - - +
305C LEU* 3.5 8.5 - - - +
306C CYS 3.1 26.8 + - - +
308C ASP* 2.9 33.1 + - - +
311C MET* 3.5 30.9 - - + +
312C LEU* 3.9 22.6 - - + +
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Residues in contact with VAL 136 (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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123C TYR* 4.8 6.5 - - + +
124C GLU* 3.8 37.8 - - + +
127C ILE* 3.9 21.8 - - + -
128C THR* 3.8 4.7 - - + +
135C LYS* 1.3 77.9 - - - +
137C LEU* 1.3 64.9 + - - +
138C PRO* 3.7 8.0 - - + +
303C ALA* 3.6 27.1 - - + -
304C VAL 3.3 13.7 - - - +
305C LEU* 3.9 19.1 - - + -
311C MET* 3.8 4.8 - - - +
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Residues in contact with LEU 137 (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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113C ARG* 5.2 6.1 - - - +
136C VAL* 1.3 74.6 - - - +
138C PRO* 1.3 81.8 - - + +
139C MET* 4.3 12.0 - - - +
148C THR* 3.8 19.3 - - + -
152C LEU* 4.6 6.1 - - + -
303C ALA* 3.6 2.6 - - - -
304C VAL* 3.0 40.4 + - + +
311C MET* 3.8 23.8 - - + +
314C ILE* 5.0 11.0 - - + -
319C HIS* 4.1 19.5 - - + +
320C GLY* 6.1 2.5 - - - -
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Residues in contact with PRO 138 (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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113C ARG* 3.1 34.7 + - - +
120C LEU* 4.3 11.4 - - + -
123C TYR* 4.8 13.7 - - + -
124C GLU* 4.4 7.0 - - - +
136C VAL* 3.7 10.3 - - + +
137C LEU* 1.3 90.6 - - + +
139C MET* 1.3 72.5 + - - +
301C VAL* 6.3 1.6 - - + -
302C SER 3.9 7.4 - - - +
303C ALA* 4.7 2.5 - - + -
321C SER* 5.1 0.2 - - - -
324C GLY* 4.0 9.4 - - - -
325C GLY* 3.9 24.0 - - - +
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Residues in contact with MET 139 (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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137C LEU* 3.8 14.3 + - + +
138C PRO* 1.3 85.1 - - - +
140C ASN* 1.3 66.6 + - - +
144C GLU* 3.7 33.7 - - + +
145C ALA* 4.5 4.3 - - - +
147C GLU* 6.5 0.2 - - + -
148C THR* 3.6 28.9 - - - +
300C PRO 4.5 0.2 - - - +
301C VAL* 3.9 5.9 - - - +
302C SER* 3.0 39.8 + - - +
303C ALA* 5.5 0.2 - - - -
304C VAL* 4.9 0.9 - - + -
319C HIS* 3.9 16.4 - - + +
320C GLY* 3.8 18.2 - - - +
321C SER* 3.9 19.3 - - - -
324C GLY* 4.3 6.0 - - - -
325C GLY 5.0 1.2 + - - -
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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