Contacts of the helix formed by residues 93 - 110 (chain B) in PDB entry 2QNJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN 4.1 1.2 + - - -
92B LEU* 1.3 75.8 - - - +
94B PRO* 1.3 75.0 - - + +
95B THR* 3.0 13.4 + - - +
96B SER* 2.7 33.6 + - - -
97B LEU* 2.9 20.5 + - - +
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Residues in contact with PRO 94 (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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93B ASN* 1.3 91.9 - - + +
95B THR* 1.3 58.9 + - - +
97B LEU* 3.4 11.9 + - + +
98B GLN* 3.1 29.3 + - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 3.0 13.2 + - - +
94B PRO* 1.3 78.1 - - - +
96B SER* 1.3 65.4 + - - +
98B GLN* 3.4 14.0 + - - +
99B LYS* 3.0 24.6 + - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.8 28.6 - - - +
93B ASN* 2.7 32.3 + - - -
95B THR* 1.3 73.0 - - - +
97B LEU* 1.3 54.1 + - - +
99B LYS* 3.2 9.4 + - - +
100B LEU* 2.7 36.6 + - - +
202B GLU* 5.9 3.1 - - - +
203B PHE* 3.6 10.2 - - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 3.8 44.2 - - + +
92B LEU* 4.3 12.6 - - + +
93B ASN 2.9 13.1 + - - +
94B PRO* 3.4 16.4 - - + +
96B SER* 1.3 78.7 - - - +
98B GLN* 1.3 60.9 + - - +
100B LEU* 3.4 14.5 - - + +
101B PHE* 3.1 48.5 + - + -
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Residues in contact with GLN 98 (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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94B PRO 3.1 17.3 + - - +
95B THR* 3.7 12.9 + - - +
96B SER 3.2 0.2 - - - -
97B LEU* 1.3 73.2 - - - +
99B LYS* 1.3 65.5 + - - +
101B PHE* 3.3 9.1 + - - +
102B ARG* 3.1 23.1 + - + +
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Residues in contact with LYS 99 (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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95B THR* 3.0 18.2 + - + +
96B SER* 3.5 6.5 - - - +
98B GLN* 1.3 78.8 - - - +
100B LEU* 1.3 62.0 + - - +
102B ARG* 3.3 7.6 + - - +
103B GLU* 2.9 43.8 + - + +
200B SER* 3.6 10.3 + - - +
202B GLU* 2.6 34.9 + - - +
203B PHE* 4.2 7.0 - - + -
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Residues in contact with LEU 100 (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 ILE* 3.7 34.1 - - + -
89B LYS* 5.0 1.3 - - + -
92B LEU* 3.8 26.2 - - + -
96B SER 2.7 20.4 + - - +
97B LEU* 3.4 14.8 - - + +
98B GLN 3.3 0.2 - - - -
99B LYS* 1.3 73.5 - - - +
101B PHE* 1.3 57.8 + - + +
103B GLU* 3.0 6.4 + - - +
104B VAL* 2.8 36.6 + - + +
128B LEU* 3.9 25.6 - - + -
199B PHE* 4.2 11.0 - - + -
203B PHE* 3.7 30.5 - - + -
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Residues in contact with PHE 101 (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 LYS* 4.7 2.2 - - + -
97B LEU* 3.1 44.8 + - + -
98B GLN* 3.3 8.5 + - - +
100B LEU* 1.3 79.7 - - + +
102B ARG* 1.3 57.5 + - - +
104B VAL* 3.3 13.6 + - + +
105B ARG* 2.9 26.3 + - - +
121B VAL* 5.6 3.6 - - + -
123B GLU* 3.2 41.5 - - - -
128B LEU* 3.9 26.5 - - + -
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Residues in contact with ARG 102 (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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274A PHE* 6.0 0.2 - - - +
98B GLN* 3.1 13.7 + - + +
99B LYS* 3.7 10.1 - - - +
101B PHE* 1.3 73.5 - - - +
103B GLU* 1.3 59.7 + - - +
105B ARG* 3.3 20.8 + - - +
106B ILE* 2.9 34.1 + - + +
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Residues in contact with GLU 103 (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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99B LYS* 2.9 25.7 + - + +
100B LEU 3.3 9.2 - - - +
102B ARG* 1.3 75.3 - - + +
104B VAL* 1.3 59.9 + - - +
106B ILE* 3.0 15.5 + - + +
107B MET* 2.8 32.3 + - - +
198B GLY 3.9 15.4 - - - +
199B PHE* 3.1 23.6 - - + -
200B SER* 2.9 46.9 + - - -
203B PHE* 3.4 18.6 - - - -
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Residues in contact with VAL 104 (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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100B LEU* 2.8 31.2 + - + +
101B PHE* 3.5 17.0 - - + +
103B GLU* 1.3 71.2 - - - +
105B ARG* 1.3 62.8 + - - +
107B MET* 3.2 9.8 + - - +
108B LYS* 3.1 32.8 + - - +
118B LEU* 4.5 4.9 - - + -
121B VAL* 4.1 27.8 - - + -
128B LEU* 4.6 8.7 - - + -
130B LEU* 3.8 34.8 - - + -
199B PHE* 5.0 2.9 - - + -
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Residues in contact with ARG 105 (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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274A PHE* 3.5 26.3 + - + +
275A TYR* 3.5 42.2 + - - +
101B PHE 2.9 14.0 + - - +
102B ARG* 3.3 21.6 - - - +
103B GLU 3.2 0.2 - - - -
104B VAL* 1.3 73.9 - - - +
106B ILE* 1.3 62.4 + - - +
108B LYS* 3.4 28.7 - - + +
109B ILE* 3.2 19.0 - - + +
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Residues in contact with ILE 106 (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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274A PHE* 4.4 30.5 - - + -
102B ARG* 2.9 20.9 + - + +
103B GLU* 3.0 17.7 + - + +
105B ARG* 1.3 71.5 - - - +
107B MET* 1.3 68.4 + - - +
109B ILE* 2.9 22.6 + - - +
110B LEU* 3.2 17.9 + - + +
174B ILE* 3.6 37.7 - - + -
197B PHE 5.3 2.0 - - - +
198B GLY* 4.5 16.2 - - - +
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Residues in contact with MET 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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85B LYS* 5.2 2.9 - - - -
103B GLU 2.8 11.9 + - - +
104B VAL* 3.2 13.9 - - - +
106B ILE* 1.3 76.4 - - - +
108B LYS* 1.3 63.7 + - - +
110B LEU* 3.0 33.7 + - + +
116B VAL 5.5 4.1 - - - +
118B LEU* 4.1 22.5 + - + +
130B LEU* 4.4 12.1 - - + -
132B MET* 3.5 38.4 - - + +
196B ASP* 5.7 1.8 - - - +
199B PHE* 3.2 51.1 - - + -
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Residues in contact with LYS 108 (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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104B VAL* 3.1 30.3 + - - +
105B ARG* 3.4 19.7 - - + +
107B MET* 1.3 78.3 - - - +
109B ILE* 1.3 57.9 + - + +
110B LEU 3.6 0.3 + - - +
111B ASN* 3.2 20.4 + - - +
118B LEU* 3.8 13.2 - - + +
121B VAL* 4.4 7.5 - - - +
353B LYS* 6.3 0.2 - - - +
354B TYR* 3.3 62.3 + - + +
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Residues in contact with ILE 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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272A ILE 6.1 1.1 - - - +
274A PHE* 3.5 53.2 - - + +
105B ARG* 3.2 21.1 - - + +
106B ILE* 2.9 12.2 + - + +
108B LYS* 1.3 76.7 - - + +
110B LEU* 1.3 66.1 + - + +
111B ASN* 3.2 8.5 + - - +
168B TYR* 3.2 9.4 + - - -
172B LYS* 3.8 26.7 - - + -
174B ILE* 5.5 0.4 - - + -
321B GLU* 4.0 5.6 - - - +
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Residues in contact with LEU 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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106B ILE* 3.6 16.4 - - + +
107B MET* 3.0 24.4 + - + +
109B ILE* 1.3 78.0 - - + +
111B ASN* 1.3 67.5 + - - +
112B HIS 4.0 2.2 + - - -
115B ILE* 3.9 29.0 - - + +
116B VAL 5.0 2.8 - - - +
117B LYS* 4.8 10.2 - - - -
118B LEU 5.3 0.3 + - - -
168B TYR* 4.0 13.2 - - + -
169B CYS* 4.2 22.9 - - - -
172B LYS* 5.0 4.9 - - + -
174B ILE* 3.8 28.0 - - + -
197B PHE* 3.8 23.3 - - + +
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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