Contacts of the helix formed by residues 95 - 101 (chain M) in PDB entry 4UJ3
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 95 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M SER 5.6 2.9 - - - -
21M GLY* 4.4 6.7 + - - -
92M ASP* 2.6 38.5 + - + +
94M ALA* 1.3 83.8 - - + +
96M HIS* 1.3 63.5 + - - +
97M LEU* 3.2 4.9 - - + +
98M THR* 2.7 45.1 + - + -
99M TYR 3.9 0.5 + - - -
125M LYS* 3.9 11.1 - - - +
133M ALA* 4.5 0.2 - - - -
134M VAL* 4.8 0.2 - - - -
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Residues in contact with HIS 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M LYS* 1.3 72.2 - - - +
97M LEU* 1.3 57.9 + - - +
99M TYR* 2.8 34.8 + + - +
100M GLU* 2.7 52.1 + - + +
133M ALA* 3.3 37.8 - - + +
134M VAL* 3.6 18.8 - - + -
138M GLU* 4.3 15.8 + - - -
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Residues in contact with LEU 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ASP* 4.9 1.6 - - - +
95M LYS* 3.1 4.5 + - + +
96M HIS* 1.3 77.3 - - - +
98M THR* 1.3 61.7 + - + +
100M GLU* 3.1 29.3 + - + +
101M ASN* 2.9 51.0 + - - +
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Residues in contact with THR 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ASP* 3.5 31.2 - - + +
20M SER 5.2 3.6 - - - +
22M VAL* 3.9 14.6 - - + +
90M VAL 4.9 1.9 - - - +
91M TYR* 3.4 11.4 - - - +
92M ASP* 2.8 36.3 + - + +
95M LYS* 2.7 37.1 + - + +
97M LEU* 1.3 79.1 - - + +
99M TYR* 1.3 59.9 + - - +
101M ASN* 3.9 3.4 + - - +
102M VAL* 3.5 13.0 + - - +
105M TRP* 5.3 1.6 - - - -
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Residues in contact with TYR 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M TYR* 4.0 25.6 - + + -
96M HIS* 2.8 24.0 + + - +
98M THR* 1.3 78.9 + - - +
100M GLU* 1.3 63.5 + - - +
101M ASN 3.1 1.8 - - - -
102M VAL* 2.8 36.3 + - + +
121M LEU* 4.8 8.3 - - + -
134M VAL* 3.7 31.9 - - + -
138M GLU* 3.3 50.0 + - + +
139M ALA* 3.9 20.6 - - + -
142M PHE* 3.4 22.4 - + + +
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M HIS* 2.7 49.5 + - + +
97M LEU* 3.4 35.1 + - + +
99M TYR* 1.3 79.8 - - - +
101M ASN* 1.3 60.0 + - - +
102M VAL 3.2 4.0 + - - -
103M GLU* 3.8 12.8 + - - +
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Residues in contact with ASN 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M ASP* 3.0 37.5 + - - +
97M LEU* 2.9 39.3 + - - +
98M THR 4.2 2.0 - - - +
99M TYR 3.1 0.2 - - - -
100M GLU* 1.3 73.8 - - - +
102M VAL* 1.3 65.5 + - - +
103M GLU 3.1 3.4 - - - -
104M ARG* 3.0 24.5 + - + +
105M TRP* 3.2 15.9 + - + +
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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