Contacts of the helix formed by residues 91 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 4.0 8.9 + - - +
89A GLY 3.6 2.0 - - - -
90A ASN* 1.3 85.1 - - + +
92A THR* 1.3 66.0 + - - +
93A ARG* 3.3 9.6 - - - -
94A VAL* 3.1 37.3 + - + +
95A TYR* 3.1 51.0 + - + +
476D ALA* 5.4 7.0 - - - -
510D SER* 3.2 50.0 - - - +
513D LEU* 4.4 2.0 - - + -
514D LEU* 4.3 17.9 - - + +
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Residues in contact with THR 92 (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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82A ILE* 5.3 1.3 - - + -
86A GLU* 3.7 27.4 - - + +
87A ARG* 4.5 4.4 - - - -
89A GLY 5.2 3.0 + - - +
90A ASN* 3.4 1.4 - - - -
91A MET* 1.3 78.7 + - - +
93A ARG* 1.3 56.8 + - - +
95A TYR* 3.0 16.5 + - + -
96A TYR* 2.8 56.5 + - + +
120A TRP* 4.7 3.8 - - + -
123A ASP* 3.3 22.7 + - - +
127A LYS* 3.1 26.7 + - - -
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Residues in contact with ARG 93 (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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90A ASN* 3.0 32.7 + - - +
91A MET* 4.3 5.6 - - - -
92A THR* 1.3 81.3 + - - +
94A VAL* 1.3 76.5 + - - +
96A TYR* 3.8 1.2 + - - +
97A LYS* 3.6 18.5 + - - +
127A LYS* 3.9 33.5 - - + +
476D ALA* 6.3 0.2 - - - +
480D ASP* 3.1 40.6 + - - -
514D LEU* 4.1 13.1 - - - +
517D HIS* 4.6 13.9 + - + -
518D TYR* 3.6 10.5 + - - -
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Residues in contact with VAL 94 (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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27A LYS* 4.3 2.8 + - - -
80A TRP* 5.0 1.8 - - + -
91A MET* 3.1 22.1 + - + +
92A THR 3.0 0.8 - - - -
93A ARG* 1.3 94.8 - - - +
95A TYR* 1.3 66.7 + - + +
97A LYS* 3.5 14.4 + - - +
513D LEU* 4.0 26.9 - - + +
514D LEU* 3.9 19.7 - - + -
517D HIS* 3.8 44.2 + - + -
551D TYR* 4.9 10.7 - - + -
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Residues in contact with TYR 95 (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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27A LYS* 2.8 27.4 + - - -
29A LEU* 3.7 4.0 - - - +
59A GLY* 4.5 4.0 - - - -
60A VAL* 3.3 34.9 - - + +
80A TRP* 3.7 17.5 - + + -
82A ILE* 3.9 26.7 - - + -
86A GLU* 3.0 41.2 + - + -
91A MET* 3.3 40.1 - - + +
92A THR* 3.0 15.7 + - + +
94A VAL* 1.3 81.5 - - + +
96A TYR* 1.3 59.2 + - + +
509D GLN* 4.8 2.8 + - - -
510D SER* 4.7 5.4 + - - -
513D LEU* 3.9 22.2 - - + +
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Residues in contact with TYR 96 (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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27A LYS* 3.9 0.2 - - - -
29A LEU* 3.5 25.1 - - + -
31A ILE* 4.2 9.7 - - + +
82A ILE* 3.9 22.4 - - + -
92A THR* 2.8 34.9 + - + +
93A ARG 4.4 2.9 - - - +
94A VAL 3.3 0.2 - - - -
95A TYR* 1.3 75.7 - - + +
97A LYS* 1.3 68.8 + - - +
98A GLU 3.3 0.5 + - - -
99A ALA* 3.1 19.0 + - - +
120A TRP* 3.4 26.1 - + - -
123A ASP* 2.6 39.4 + - - +
124A LEU* 3.7 28.7 - - + -
127A LYS* 4.0 16.4 - - + +
128A VAL* 3.2 22.5 - - + +
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Residues in contact with LYS 97 (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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27A LYS* 2.5 29.3 + - - +
93A ARG 3.6 10.9 + - - +
94A VAL 3.5 14.5 + - - +
95A TYR 3.3 3.2 - - - -
96A TYR* 1.3 78.4 - - - +
98A GLU* 1.3 85.1 + - + +
99A ALA 3.0 2.6 + - - -
127A LYS 5.5 2.0 - - - -
128A VAL* 4.9 3.6 - - - -
517D HIS* 3.9 37.8 + - + +
519D LYS* 3.4 27.1 - - - +
551D TYR* 4.3 13.4 + - + +
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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