Contacts of the helix formed by residues 93 - 103 (chain O) in PDB entry 2D2C
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 ASN 93 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91O LEU* 2.8 26.1 + - - +
92O PRO* 1.3 76.7 - - - +
94O LYS* 1.3 99.5 + - + +
95O LEU* 5.1 4.0 - - - +
97O GLY* 5.3 0.4 - - - -
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Residues in contact with LYS 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O LEU* 5.2 1.1 - - + -
92O PRO* 3.7 16.5 + - - +
93O ASN* 1.3 99.0 + - + +
95O LEU* 1.3 63.9 + - - +
96O LEU* 2.6 28.2 + - + +
97O GLY* 3.0 13.9 + - - -
98O VAL* 3.9 3.8 + - - +
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Residues in contact with LEU 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157N ALA* 3.5 27.8 - - + -
158N ILE* 3.8 34.3 - - + +
159N PRO* 4.7 7.0 - - + -
93O ASN* 5.1 3.6 - - - +
94O LYS* 1.3 74.5 - - - +
96O LEU* 1.3 56.4 + - - +
97O GLY 3.1 0.7 - - - -
98O VAL* 2.9 15.2 + - + -
99O LEU* 2.3 43.7 + - + +
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Residues in contact with LEU 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O LEU* 3.0 31.0 - - + -
94O LYS* 2.6 24.9 - - + +
95O LEU 1.3 76.3 - - - +
97O GLY* 1.3 69.6 + - - +
99O LEU* 4.3 17.0 - - + -
100O LEU* 2.8 46.4 + - + +
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Residues in contact with GLY 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O ILE* 3.9 8.5 - - - +
88O LEU* 4.4 20.1 - - - +
91O LEU* 3.5 26.3 - - - +
93O ASN 4.5 0.4 - - - -
94O LYS 3.0 9.7 + - - -
96O LEU* 1.3 82.1 - - - +
98O VAL* 1.3 65.6 + - - +
101O MET* 3.2 16.8 + - - +
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Residues in contact with VAL 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N VAL* 3.9 34.1 - - + +
155N PRO* 6.3 0.7 - - + -
157N ALA* 4.7 10.1 - - + -
158N ILE* 4.0 25.6 - - + -
88O LEU* 4.5 6.2 - - + +
94O LYS 3.9 2.9 + - - +
95O LEU* 2.9 20.8 + - + +
97O GLY* 1.3 72.4 - - - +
99O LEU* 1.3 71.2 + - - +
101O MET* 2.6 36.5 + - + +
102O ALA* 2.9 6.0 + - + -
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Residues in contact with LEU 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O LEU* 2.3 33.1 + - + +
96O LEU* 4.1 15.3 - - + +
98O VAL* 1.3 68.2 - - - +
100O LEU* 1.3 64.6 + - - +
102O ALA* 2.4 37.8 + - + -
103O SER* 2.5 30.7 + - - +
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Residues in contact with LEU 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O ILE* 4.1 25.8 - - + -
91O LEU* 3.9 11.7 - - + -
96O LEU* 2.8 46.3 + - + +
97O GLY 4.0 1.6 - - - +
99O LEU* 1.3 79.8 - - + +
101O MET* 1.3 57.2 + - - +
103O SER* 2.9 29.8 + - - -
104O VAL* 3.7 3.9 + - + +
1201O CLA 5.1 16.2 - - + -
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Residues in contact with MET 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N VAL* 4.3 10.8 - - + -
81O LEU* 5.3 4.3 - - + -
84O VAL* 3.7 37.5 - - + +
87O ILE* 4.5 13.6 - - + +
88O LEU* 3.9 29.4 - - + -
97O GLY 3.2 7.2 + - - +
98O VAL* 2.6 31.4 + - + +
100O LEU* 1.3 71.5 - - - +
102O ALA* 1.3 64.2 + - + +
103O SER 2.8 4.7 - - - -
104O VAL* 2.8 34.1 + - + +
105O PRO* 3.1 4.9 - - - +
1201O CLA 3.3 35.7 - - + +
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Residues in contact with ALA 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98O VAL* 4.0 10.1 - - + +
99O LEU* 2.4 26.8 + - + +
101O MET* 1.3 81.2 - - + +
103O SER* 1.3 53.9 + - - -
105O PRO* 2.9 28.0 - - - +
106O LEU* 3.4 18.6 + - + +
1201O CLA 4.0 23.5 - - + +
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Residues in contact with SER 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O LEU* 2.5 37.3 + - - +
100O LEU* 2.9 26.7 + - - -
101O MET 2.8 0.6 - - - -
102O ALA* 1.3 79.3 - - - +
104O VAL* 1.3 58.6 + - - +
105O PRO 3.5 0.4 - - - -
106O LEU* 4.8 0.9 - - - -
107O GLY* 3.4 28.4 - - - +
108O LEU 4.2 0.2 + - - -
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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