Contacts of the helix formed by residues 106 - 117 (chain B) in PDB entry 3R9X
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 VAL 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 5.4 1.8 - - - +
103B PRO* 2.9 25.0 + - + -
105B ASN* 1.3 110.2 + - - +
107B ALA* 1.3 65.5 + - - +
108B SER 3.3 2.5 - - - -
109B LEU* 3.1 26.3 + - + +
110B ILE* 2.9 35.1 - - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.8 31.1 - - + +
103B PRO 3.4 3.4 + - - +
104B TYR* 3.2 18.7 + - - +
106B VAL* 1.3 76.4 - - - +
108B SER* 1.3 63.9 + - - +
110B ILE* 3.2 5.5 + - - +
111B ILE* 3.0 30.8 + - + +
128B VAL* 4.4 12.8 - - + -
129B GLN 6.0 0.4 - - - +
132B VAL* 4.7 15.3 - - + -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR 5.0 0.2 + - - -
106B VAL 3.3 0.4 - - - -
107B ALA* 1.3 76.5 - - - +
109B LEU* 1.3 67.8 + - - +
111B ILE* 3.2 4.2 + - - +
112B GLU* 2.8 36.1 + - - +
132B VAL* 5.5 7.5 - - - +
144B TRP* 6.0 2.2 - - - -
145B LEU* 3.5 27.6 - - - +
1510C C 5.6 4.3 + - - -
1511C G 6.1 1.1 - - - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 3.4 27.6 - - - +
105B ASN 4.5 5.2 - - - +
106B VAL* 3.1 31.6 + - + +
108B SER* 1.3 85.3 - - - +
110B ILE* 1.3 61.8 + - + +
112B GLU* 3.8 16.3 - - - +
113B ASN* 3.2 18.0 + - - +
1509C C 4.8 8.3 - - - +
1510C C 4.6 34.5 - - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.8 16.8 - - + -
38B GLY* 6.2 0.4 - - - -
84B ALA* 3.7 26.7 - - + -
85B SER* 3.6 22.9 - - - +
89B PHE* 5.1 4.2 - - + -
98B VAL* 6.0 0.2 - - + -
102B LEU* 3.8 30.3 - - + -
103B PRO* 5.7 1.1 - - + -
106B VAL* 2.9 46.3 + - + +
107B ALA* 3.2 5.8 + - - +
109B LEU* 1.3 73.8 - - - +
111B ILE* 1.3 56.7 + - - +
113B ASN* 3.3 4.0 + - - +
114B THR* 2.6 41.9 + - - +
126B PHE* 4.3 6.3 - - + -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.8 20.2 - - + -
107B ALA* 3.0 27.4 + - + +
108B SER* 3.6 7.2 - - - +
110B ILE* 1.3 71.8 - - - +
112B GLU* 1.3 67.8 + - - +
114B THR* 3.2 11.2 + - - -
115B VAL* 3.0 22.7 + - + +
126B PHE* 4.4 15.7 - - + -
128B VAL* 4.6 11.2 - - + -
132B VAL* 4.8 4.0 - - + -
136B LEU* 3.8 27.1 - - + -
145B LEU* 3.9 9.4 - - + -
149B VAL* 3.6 29.4 - - + -
177B ILE* 5.1 1.1 - - + -
179B LEU* 4.9 9.0 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 2.8 19.4 + - - +
109B LEU* 3.8 17.1 - - - +
111B ILE* 1.3 77.6 - - - +
113B ASN* 1.3 63.6 + - - +
115B VAL* 3.0 18.1 + - - +
116B TYR* 3.1 48.3 + - + +
144B TRP* 3.3 36.7 - - + -
145B LEU* 4.2 10.1 - - + -
148B PHE* 4.2 3.3 - - + -
194B LYS* 3.3 14.0 - - - -
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA 2.6 30.5 + - - -
85B SER* 3.4 9.4 - - - +
86B LYS* 3.0 18.6 - - - +
87B PHE 3.3 14.8 + - - +
89B PHE* 3.4 7.8 - - - -
109B LEU 3.2 13.3 + - - +
110B ILE 3.5 8.3 + - - +
112B GLU* 1.3 79.6 - - - +
114B THR* 1.3 60.9 + - - +
116B TYR* 3.3 22.8 + - - +
117B ASN* 2.8 35.5 + - - -
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.8 15.6 - - + -
98B VAL* 4.5 17.7 - - + +
110B ILE* 2.6 25.0 + - - +
111B ILE* 3.2 12.1 + - - -
113B ASN* 1.3 76.5 - - - +
115B VAL* 1.3 59.9 + - + +
117B ASN* 2.9 20.8 + - - +
118B LYS* 3.2 9.2 + - - -
121B VAL* 4.2 24.8 - - + +
124B ALA* 4.8 8.7 - - + -
126B PHE* 4.0 13.9 - - + -
153B TYR* 4.6 5.3 + - + +
179B LEU* 5.8 3.8 - - + -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 3.0 14.8 + - + +
112B GLU 3.0 8.7 + - - +
114B THR* 1.3 74.7 - - - +
116B TYR* 1.3 61.2 + - - +
118B LYS* 2.8 35.5 - - - +
148B PHE* 3.4 23.8 - - + +
149B VAL* 3.7 27.8 - - + -
152B PHE* 3.3 33.9 - - + -
153B TYR* 4.3 19.1 - - + -
179B LEU* 5.7 3.1 - - + -
190B LEU* 3.8 2.1 - - - +
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU* 3.1 57.5 + - + -
113B ASN* 3.4 18.8 - - - +
114B THR 3.3 0.2 - - - -
115B VAL* 1.3 77.2 - - - +
117B ASN* 1.3 62.2 + - - +
118B LYS 3.4 2.4 + - - -
119B ASP* 3.5 12.6 - - - +
148B PHE* 4.4 13.4 - + - -
190B LEU* 3.9 24.4 - - + +
191B LYS* 4.0 40.2 - - + +
194B LYS* 3.2 22.8 - - + +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE 3.9 1.8 + - - -
88B PRO* 3.9 7.9 - - - +
89B PHE* 3.4 46.9 + - + +
90B CYS* 3.7 20.8 + - - +
113B ASN* 2.8 36.8 + - - -
114B THR 2.9 11.2 + - - +
116B TYR* 1.3 79.6 - - - +
118B LYS* 1.3 63.0 + - - +
119B ASP* 3.0 6.1 + - - -
120B CYS* 3.2 10.6 + - - -
121B VAL* 3.0 14.5 - - + +
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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