Contacts of the helix formed by residues 116 - 121 (chain A) in PDB entry 2CAS
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 ALA 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ALA 3.3 1.8 + - - -
115A ASN* 1.3 77.2 - - - +
117A TRP* 1.3 65.8 + - - +
118A GLY 3.3 0.2 - - - -
119A VAL* 3.1 13.7 + - + +
120A TRP* 3.4 12.3 - - - -
189A ALA* 4.5 3.6 - - + -
194A THR* 3.8 24.7 - - + +
197A PHE* 4.1 10.3 - - + -
465A PRO 3.9 9.2 - - - +
466A ASN 4.5 4.9 - - - +
467A GLY 3.1 16.6 - - - +
469A ILE* 3.9 6.9 - - - +
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Residues in contact with TRP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA* 1.3 70.3 - - - +
118A GLY* 1.3 62.5 + - - +
119A VAL 3.0 1.7 + - - -
120A TRP* 3.0 5.9 + - - +
121A PHE* 3.0 49.7 + + - +
126A TRP* 3.3 27.4 - + - -
136A LEU* 3.9 17.9 - - + -
462A PRO* 3.8 28.4 - - + +
463A VAL 3.5 21.5 - - - +
464A TYR* 3.6 20.8 - - + -
465A PRO* 3.5 6.7 + - + +
467A GLY 3.1 26.0 + - - -
468A GLN 3.7 12.5 + - - -
469A ILE* 3.8 20.3 - - + +
487A PRO* 4.3 5.9 - - + +
488A PHE* 3.8 31.4 - + - -
535A PHE* 3.7 15.5 - + - -
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 4.6 0.3 + - - -
116A ALA 3.3 0.4 - - - -
117A TRP* 1.3 75.6 - - - +
119A VAL* 1.3 58.4 + - - +
120A TRP 3.7 0.2 + - - -
121A PHE 3.8 9.7 - - - +
197A PHE* 3.3 38.2 - - - +
464A TYR* 4.0 7.0 - - - -
465A PRO* 3.0 34.9 + - - +
571A ILE* 5.2 1.3 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 4.9 2.4 + - - -
65A SER* 2.8 36.1 + - - +
67A ARG* 3.2 18.5 + - - +
114A ALA* 3.7 41.1 - - + +
116A ALA* 3.5 17.7 - - + +
117A TRP 3.0 1.0 + - - -
118A GLY* 1.3 77.0 - - - +
120A TRP* 1.3 66.8 + - + +
194A THR* 4.5 0.4 - - - -
195A LEU* 4.0 20.4 - - + +
196A GLY 4.7 2.7 - - - +
197A PHE* 3.8 19.3 - - + -
529A TRP* 4.4 5.8 - - + -
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Residues in contact with TRP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 5.4 3.7 + - - -
49A THR* 3.7 15.6 - - - +
63A ALA* 3.4 35.7 - - + +
64A ASN 4.9 4.3 - - - +
65A SER* 3.5 19.1 - - - -
114A ALA* 2.8 25.6 + - + -
115A ASN* 4.9 0.2 - - - +
116A ALA 3.4 9.4 - - - -
117A TRP 3.0 3.7 + - - +
118A GLY 4.8 0.2 - - - -
119A VAL* 1.3 86.2 - - + +
121A PHE* 1.3 76.9 + - + +
141A PHE* 3.7 22.2 - + - -
469A ILE* 3.4 26.2 - - + +
470A TRP* 5.2 2.3 - + - -
529A TRP* 3.8 15.0 - + - -
531A GLY* 3.3 44.2 - - - -
532A LYS 3.5 3.6 - - - -
533A LEU* 3.6 25.9 - - + +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 4.4 6.7 - - + -
61A ILE* 3.8 22.7 - - + -
63A ALA* 3.8 13.9 - - + -
117A TRP* 3.0 46.4 + + - -
118A GLY 3.8 11.5 - - - +
120A TRP* 1.3 91.4 - - + +
122A ASN* 1.3 58.3 + - - +
125A ASP* 3.6 26.7 - - + -
126A TRP* 4.1 12.6 - + + -
129A ILE* 3.8 20.6 - - + -
136A LEU* 5.9 0.2 - - + -
464A TYR* 2.7 34.2 + - + -
535A PHE* 3.6 31.4 - + - -
571A ILE* 5.7 0.3 - - - +
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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