Contacts of the helix formed by residues 91 - 97 (chain C) in PDB entry 4CYM
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 MET 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C GLU* 4.0 8.0 + - - +
89C GLY* 3.6 2.0 - - - -
90C ASN* 1.3 86.1 - - + +
92C THR* 1.3 65.6 + - - +
93C ARG* 3.3 10.1 - - - -
94C VAL* 3.0 40.6 + - + +
95C TYR* 3.1 49.5 + - + +
476F ALA* 5.6 4.7 - - - -
510F SER* 3.3 45.5 - - - +
513F LEU* 4.4 2.2 - - + -
514F LEU* 4.3 17.9 - - + +
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Residues in contact with THR 92 (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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82C ILE* 5.2 0.9 - - + -
86C GLU* 3.7 27.6 - - + +
87C ARG* 4.5 4.9 - - - +
89C GLY 5.3 3.0 + - - +
90C ASN* 3.4 1.8 - - - -
91C MET* 1.3 77.2 + - - +
93C ARG* 1.3 57.2 + - - +
95C TYR* 2.9 16.7 + - + -
96C TYR* 2.8 55.7 + - + +
120C TRP* 4.7 4.0 - - + -
123C ASP* 3.3 22.3 + - - +
127C LYS* 3.1 26.9 + - - -
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Residues in contact with ARG 93 (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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90C ASN* 3.0 33.9 + - - +
91C MET* 5.0 5.3 - - - -
92C THR* 1.3 81.5 + - - +
94C VAL* 1.3 76.1 + - - +
96C TYR* 4.3 1.3 - - - +
97C LYS* 3.6 17.7 + - - +
127C LYS* 3.9 33.9 - - + +
480F ASP* 3.3 38.4 + - - -
514F LEU* 4.3 11.9 - - - +
517F HIS* 4.5 16.6 + - - +
518F TYR* 3.6 10.9 + - - -
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Residues in contact with VAL 94 (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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27C LYS* 4.3 3.3 + - - -
80C TRP* 5.0 1.5 - - + -
91C MET* 3.0 23.5 + - + +
92C THR 3.0 1.2 - - - -
93C ARG* 1.3 93.4 - - - +
95C TYR* 1.3 68.0 + - + +
97C LYS* 3.5 15.6 + - - +
513F LEU* 4.1 23.8 - - + +
514F LEU* 4.1 17.0 - - + -
517F HIS* 3.8 44.9 - - + +
551F TYR* 4.8 11.8 - - + -
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Residues in contact with TYR 95 (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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27C LYS* 2.8 27.2 + - - -
29C LEU* 3.7 4.2 - - - +
59C GLY* 4.5 4.0 - - - -
60C VAL* 3.2 35.6 - - + +
80C TRP* 3.6 18.2 - + + -
82C ILE* 3.9 27.1 - - + -
86C GLU* 3.0 41.6 + - + -
91C MET* 3.3 40.6 - - + +
92C THR* 2.9 17.0 + - + +
94C VAL* 1.3 82.1 - - + +
96C TYR* 1.3 58.1 + - + +
509F GLN* 4.9 2.4 + - - -
510F SER* 5.4 4.7 + - - -
513F LEU* 4.0 22.2 - - + +
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Residues in contact with TYR 96 (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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27C LYS* 3.9 0.4 - - - -
29C LEU* 3.5 25.8 - - + -
31C ILE* 4.3 9.4 - - + +
82C ILE* 3.8 21.3 - - + -
92C THR* 2.8 33.5 + - + +
93C ARG 4.4 3.1 - - - +
95C TYR* 1.3 74.8 - - - +
97C LYS* 1.3 68.6 + - - +
98C GLU 3.3 0.5 + - - -
99C ALA* 3.1 19.2 + - - +
120C TRP* 3.4 26.3 - + - -
123C ASP* 2.6 38.9 + - - +
124C LEU* 3.7 29.2 - - + -
127C LYS* 4.0 16.6 - - + -
128C VAL* 3.2 23.0 - - + +
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Residues in contact with LYS 97 (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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27C LYS* 2.5 30.6 + - - +
93C ARG 3.6 11.7 + - - +
94C VAL 3.5 13.8 + - - +
95C TYR 3.2 2.8 - - - -
96C TYR* 1.3 78.3 - - - +
98C GLU* 1.3 86.4 + - + +
99C ALA 3.0 2.6 + - - -
127C LYS 5.6 1.3 - - - -
128C VAL* 4.9 3.6 - - - -
517F HIS* 4.0 35.9 + - + +
519F LYS* 4.9 14.5 - - - +
551F TYR* 4.1 17.4 + - + +
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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