Contacts of the helix formed by residues 106 - 117 (chain I) in PDB entry 5OA3
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 SER 106 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104I ILE 3.6 0.2 + - - -
105I ASP* 1.3 73.9 - - - +
107I THR* 1.3 65.8 + - - +
108I PRO* 3.6 1.3 - - - -
109I TYR* 3.4 6.0 + - - +
110I ARG* 3.0 26.9 + - - +
165I GLN 4.7 0.7 - - - -
166I PHE* 3.1 35.4 + - - -
169I GLY* 3.1 34.5 + - - -
170I LYS 4.3 0.7 - - - -
171I LEU* 4.4 13.7 - - - -
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Residues in contact with THR 107 (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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105I ASP* 3.6 16.1 + - + +
106I SER* 1.3 76.1 - - - +
108I PRO* 1.4 74.7 - - - +
110I ARG* 3.0 29.7 + - - +
111I GLN* 2.9 39.7 + - - +
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Residues in contact with PRO 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I ARG* 4.3 23.9 - - + +
75I LYS 4.4 7.4 - - - +
76I THR* 3.6 37.5 - - + +
105I ASP 4.0 0.7 - - - +
106I SER 3.6 2.2 - - - -
107I THR* 1.4 98.5 - - - +
109I TYR* 1.3 63.4 + - + +
111I GLN* 3.5 12.8 + - + +
112I TRP* 2.9 28.9 + - - +
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Residues in contact with TYR 109 (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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65I PHE* 2.5 45.9 + - - +
67I TRP* 3.5 33.2 - + + -
72I CYS* 3.8 22.7 - - - -
74I ARG* 3.7 14.6 + - + -
76I THR* 3.8 14.8 - - - -
104I ILE* 4.1 17.7 - - + -
105I ASP 4.0 11.2 - - - -
106I SER 3.7 4.7 - - - +
107I THR 3.2 0.2 - - - -
108I PRO* 1.3 80.2 - - + +
110I ARG* 1.3 57.3 + - - +
112I TRP* 3.2 9.1 + + - +
113I TYR* 2.9 30.2 + - - +
166I PHE* 4.0 17.7 - - + -
171I LEU* 3.8 18.4 - - + -
189I VAL* 4.1 6.0 - - + +
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Residues in contact with ARG 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I SER* 3.0 27.5 + - - +
107I THR* 3.6 30.2 + - - +
109I TYR* 1.3 76.4 - - - +
111I GLN* 1.3 65.0 + - - +
113I TYR* 3.7 5.4 - - - +
114I GLU* 2.9 42.0 + - - +
121I LEU* 3.2 40.5 + - + +
122I GLY* 5.0 7.5 + - - -
123I ARG* 3.7 34.1 - - - +
133I GLU* 5.2 1.2 + - - -
166I PHE* 4.4 12.5 + - + -
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Residues in contact with GLN 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I THR* 2.9 36.8 + - - +
108I PRO* 3.7 8.9 - - - +
110I ARG* 1.3 85.4 - - + +
112I TRP* 1.3 61.9 + - - +
114I GLU* 3.8 6.8 - - - +
115I SER* 2.9 25.1 + - - -
123I ARG* 6.2 0.9 - - - +
136I ILE* 5.9 0.2 - - - +
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Residues in contact with TRP 112 (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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67I TRP* 4.1 13.0 - + - -
70I GLU* 3.6 39.5 - - + -
71I CYS 5.0 2.0 - - - -
72I CYS* 4.2 24.7 - - + +
74I ARG* 3.3 37.6 - - - +
108I PRO 2.9 17.8 + - - +
109I TYR* 3.6 8.5 - - - +
111I GLN* 1.3 76.4 - - - +
113I TYR* 1.3 93.4 + + + +
115I SER* 3.3 8.0 + - - -
116I HIS* 2.9 59.3 + + + +
117I TYR* 4.5 5.6 - + - -
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Residues in contact with TYR 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I TRP* 5.4 3.8 - + - +
70I GLU* 5.0 11.2 - - + -
109I TYR 2.9 16.0 + - - +
110I ARG 3.7 3.4 - - - +
112I TRP* 1.3 95.6 - + + +
114I GLU* 1.3 61.6 + - - +
116I HIS* 3.0 2.8 + - - +
117I TYR* 2.9 60.5 + + + +
119I LEU* 4.3 25.2 - - + +
120I PRO 4.8 1.6 - - - -
121I LEU* 3.4 40.4 - - + -
156I ALA* 3.2 29.1 + - + +
157I LYS* 4.8 0.7 - - - -
158I ILE* 4.2 22.9 - - + +
166I PHE* 6.2 0.9 - - + -
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Residues in contact with GLU 114 (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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110I ARG* 2.9 29.6 + - + +
111I GLN* 4.0 5.4 - - - +
113I TYR* 1.3 74.9 - - - +
115I SER* 1.3 57.7 + - - +
118I ALA* 3.2 25.4 - - - +
119I LEU 3.2 22.8 - - - +
120I PRO* 3.5 4.3 - - - +
121I LEU* 3.2 27.2 + - + -
123I ARG* 2.5 39.1 + - - -
133I GLU* 3.6 8.5 - - - +
136I ILE* 4.2 12.8 - - + +
137I LEU* 4.0 18.3 - - + +
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Residues in contact with SER 115 (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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111I GLN 2.9 17.2 + - - -
112I TRP* 3.5 9.0 - - - -
113I TYR 3.1 0.2 - - - -
114I GLU* 1.3 80.6 - - - +
116I HIS* 1.3 62.5 + - - +
118I ALA* 4.9 0.9 - - - +
136I ILE* 4.6 13.8 - - - +
149I TYR* 3.6 18.9 + - - -
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Residues in contact with HIS 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I GLU 6.0 0.2 - - - -
112I TRP* 2.9 50.6 + + + +
113I TYR* 3.0 3.6 + - - +
115I SER* 1.3 77.1 - - - +
117I TYR* 1.3 87.9 + + + +
149I TYR* 3.0 14.2 - - - -
152I ARG* 2.9 72.1 + - - +
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Residues in contact with TYR 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I GLU* 2.9 27.5 + - - +
112I TRP* 4.5 6.0 - + - -
113I TYR* 2.9 54.6 + + + +
116I HIS* 1.3 102.4 + + + +
118I ALA* 1.3 72.2 - - - +
119I LEU* 3.3 16.1 - - + +
149I TYR* 4.3 5.8 - - - +
152I ARG* 3.5 42.0 - - + -
153I LYS* 4.2 12.3 - - - +
155I ASN* 4.9 4.9 - - + +
156I ALA* 3.4 26.9 - - + -
21L LYS* 3.7 6.8 + - - -
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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