Contacts of the helix formed by residues 115 - 123 (chain I) in PDB entry 5A15
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 LEU 115 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I ILE* 3.9 26.9 - - + -
49I SER* 4.0 11.7 - - - -
51I LEU* 6.1 1.8 - - + -
85I ILE* 4.0 29.6 - - + -
88I TYR* 4.1 14.4 - - + -
89I LEU* 4.1 11.9 - - + -
110I ALA* 3.0 9.4 + - + +
113I PHE* 3.9 20.9 - - + +
114I GLN* 1.3 81.6 - - - +
116I PRO* 1.3 68.3 - - - +
117I ASP 3.3 2.2 - - - -
118I LEU* 3.1 30.1 + - + -
119I VAL* 3.1 23.5 + - - +
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Residues in contact with PRO 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLN* 2.9 37.2 - - + +
46I ILE* 5.5 7.4 - - + -
114I GLN* 3.4 13.9 - - + +
115I LEU* 1.3 84.4 - - - +
117I ASP* 1.3 64.1 - - - +
119I VAL* 3.3 10.3 + - + +
120I LYS* 3.0 26.5 + - - +
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Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 3.5 35.1 + - - -
111C GLU* 4.8 9.0 - - - +
112C TYR* 5.6 2.1 - - - -
93D GLN* 6.2 1.3 - - - -
88I TYR* 3.3 19.2 + - + +
115I LEU 3.3 0.6 - - - -
116I PRO* 1.3 83.3 - - - +
118I LEU* 1.3 57.3 + - - +
120I LYS* 3.3 8.8 + - - +
121I LEU* 3.0 34.1 + - + +
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Residues in contact with LEU 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I TYR 5.0 0.4 - - - +
85I ILE* 3.8 30.3 - - + -
88I TYR* 3.7 51.0 + - + -
94I VAL* 4.3 13.9 - - + -
96I LEU* 6.4 0.2 - - + -
106I LEU* 5.3 4.5 - - + -
110I ALA* 3.8 13.0 - - + -
115I LEU* 3.1 16.4 + - + +
117I ASP* 1.3 75.6 - - - +
119I VAL* 1.3 66.1 + - - +
121I LEU* 3.3 11.4 + - + +
122I LEU* 3.1 41.9 + - + +
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Residues in contact with VAL 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I LYS* 4.3 8.7 - - + +
110I ALA* 3.4 35.0 - - + +
111I GLU* 3.5 31.6 - - + +
115I LEU 3.1 16.2 + - - +
116I PRO* 3.3 9.8 + - + +
118I LEU* 1.3 75.8 - - - +
120I LYS* 1.3 62.5 + - - +
122I LEU* 3.2 5.6 + - - +
123I THR* 3.0 31.0 + - + +
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Residues in contact with LYS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I PRO 3.0 14.0 + - - +
117I ASP* 3.4 13.0 - - - +
118I LEU 3.2 0.2 - - - -
119I VAL* 1.3 78.7 - - - +
121I LEU* 1.3 65.0 + - + +
123I THR* 2.5 31.0 + - - +
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Residues in contact with LEU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I TYR* 4.5 14.8 - - + +
92I ARG 5.2 4.9 - - - +
93I GLN* 5.4 4.9 - - - -
94I VAL 5.8 1.3 - - - +
117I ASP* 3.0 21.5 + - + +
118I LEU* 3.3 21.5 + - + +
120I LYS* 1.3 80.4 - - + +
122I LEU* 1.3 63.9 + - + +
123I THR 3.7 4.0 + - - +
124I PRO* 5.7 0.2 - - - +
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Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I LEU* 4.4 17.7 - - + -
103I LYS* 4.3 22.6 - - + +
104I GLY* 6.0 0.3 - - - -
106I LEU* 3.6 32.5 - - + +
107I LYS* 3.4 48.0 - - + +
110I ALA* 4.2 2.0 - - + -
118I LEU* 3.1 38.3 + - + +
119I VAL 3.7 2.9 - - - +
120I LYS 3.2 0.2 - - - -
121I LEU* 1.3 78.2 - - + +
123I THR* 1.3 62.4 + - - +
124I PRO* 3.5 8.2 - - - +
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Residues in contact with THR 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I LYS* 3.3 34.1 - - - +
119I VAL* 3.0 22.4 + - + +
120I LYS* 2.5 35.5 + - - +
121I LEU 4.1 4.0 - - - +
122I LEU* 1.3 76.7 - - - +
124I PRO* 1.3 72.5 - - - +
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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