Contacts of the helix formed by residues 104 - 118 (chain B) in PDB entry 2QU7
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 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B SER* 3.0 22.1 + - - +
102B GLU* 2.9 6.9 + - + +
103B GLU* 1.3 78.7 - - - +
105B GLU* 1.3 59.4 + - - +
106B ASP* 2.8 38.7 + - - +
107B LYS* 2.9 16.0 + - + -
108B GLN* 3.1 21.3 + - - +
128B VAL* 4.3 1.3 - - - -
223B LEU* 4.4 15.8 - - + +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU 3.9 2.4 + - - -
104B ASN* 1.3 73.8 + - - +
106B ASP* 1.3 64.2 - - - +
108B GLN* 3.4 9.5 + - - +
109B GLN* 3.0 27.0 + - - +
128B VAL* 3.8 19.2 - - + +
129B LYS* 3.3 50.1 + - - +
131B LYS 4.6 2.6 - - - +
132B PHE* 3.5 32.1 - - + +
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN* 2.8 12.0 + - - +
105B GLU* 1.3 77.4 - - - +
107B LYS* 1.3 61.0 + - - +
109B GLN* 3.3 7.4 + - - +
110B ASP* 2.9 38.8 + - - +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 4.9 10.2 + - - -
90A GLN* 3.1 35.1 + - + +
94A LEU 4.7 0.2 + - - -
95A HIS* 2.8 46.0 + - + +
96A VAL 4.8 3.0 + - - +
100B SER 3.7 15.7 - - - -
101B SER* 3.7 26.0 - - - +
104B ASN* 2.9 22.3 + - + +
106B ASP* 1.3 73.2 - - - +
108B GLN* 1.3 64.9 + - - +
110B ASP* 3.2 8.0 + - - +
111B LEU* 2.9 37.8 + - + +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.6 4.7 - - + +
101B SER* 3.9 12.1 + - - -
104B ASN 3.1 15.3 + - - +
105B GLU* 3.6 17.1 + - - +
106B ASP 3.3 0.4 - - - -
107B LYS* 1.3 75.6 - - - +
109B GLN* 1.3 64.1 + - - +
111B LEU* 3.2 8.0 + - - +
112B ILE* 3.0 34.1 + - + +
125B LEU* 3.9 18.3 - - + +
126B VAL 3.9 1.7 - - - +
127B PRO* 3.5 6.7 - - - +
128B VAL* 2.8 39.2 + - + +
132B PHE* 3.7 42.4 - - - +
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Residues in contact with GLN 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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105B GLU* 3.0 14.4 + - + +
106B ASP* 3.6 10.5 - - - +
107B LYS 3.3 0.2 - - - -
108B GLN* 1.3 77.9 - - - +
110B ASP* 1.3 66.2 + - - +
112B ILE* 3.4 4.3 + - - +
113B GLU* 3.0 31.7 + - + +
132B PHE* 4.9 10.7 - - + -
135B LYS* 3.6 31.8 + - - +
138B TRP* 4.0 28.1 - - + -
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Residues in contact with ASP 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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93A HIS* 5.8 2.3 + - - -
95A HIS* 3.6 30.0 - - + +
106B ASP* 2.9 25.6 + - - +
107B LYS* 3.2 10.1 + - - +
109B GLN* 1.3 79.7 - - - +
111B LEU* 1.3 56.6 + - - +
113B GLU* 3.6 15.7 + - - +
114B THR* 2.9 33.0 + - - -
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Residues in contact with LEU 111 (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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66A ILE* 6.1 0.7 - - + -
95A HIS* 3.8 33.4 - - + +
96A VAL 5.4 0.4 - - - +
70B ILE* 4.0 24.9 - - + -
99B ALA* 3.7 32.1 - - + -
100B SER 3.8 24.9 - - - +
101B SER* 4.1 4.9 - - - +
107B LYS* 2.9 27.1 + - + +
108B GLN* 3.2 4.2 + - - +
110B ASP* 1.3 73.5 - - - +
112B ILE* 1.3 66.2 + - - +
114B THR* 3.3 4.8 + - - +
115B PHE* 3.0 39.7 + - + -
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Residues in contact with ILE 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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70B ILE* 3.7 21.8 - - + -
108B GLN* 3.0 33.9 + - + +
109B GLN 4.0 2.7 - - - +
111B LEU* 1.3 74.4 - - - +
113B GLU* 1.3 58.4 + - - +
115B PHE* 3.1 2.6 + - - +
116B VAL* 2.8 39.3 + - + +
123B ILE* 4.3 13.2 - - + -
125B LEU* 4.2 16.8 - - + -
132B PHE* 4.0 27.6 - - + -
134B MET* 4.4 9.0 - - + -
138B TRP* 3.5 41.5 - - + -
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Residues in contact with GLU 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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109B GLN* 3.0 24.4 + - + +
110B ASP* 3.8 16.4 - - - +
112B ILE* 1.3 77.3 - - - +
114B THR* 1.3 59.8 + - - +
116B VAL* 3.9 2.9 - - - +
117B SER* 3.1 28.1 + - - -
138B TRP* 4.2 21.3 + - + +
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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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64A SER* 5.0 1.1 - - - -
65A ASN* 2.7 47.6 + - - +
66A ILE* 3.2 26.9 - - + -
95A HIS* 3.8 5.3 - - - -
110B ASP 2.9 19.0 + - - -
111B LEU* 3.8 6.5 - - - -
112B ILE 3.3 0.2 - - - -
113B GLU* 1.3 78.1 - - - +
115B PHE* 1.3 58.8 + - - +
117B SER* 3.3 6.9 + - - -
118B GLN* 2.9 31.8 + - + +
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Residues in contact with PHE 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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66A ILE* 3.5 25.4 - - + -
97A ALA* 4.5 13.7 - - + -
66B ILE* 5.4 5.4 - - + -
68B ALA* 3.5 28.9 - - + -
69B PHE 5.6 0.2 - - - -
70B ILE* 3.9 21.8 - - + -
97B ALA* 5.5 4.3 - - + -
99B ALA* 4.1 24.9 - - + -
111B LEU* 3.0 36.4 + - + +
112B ILE 3.8 2.9 - - - +
114B THR* 1.3 73.0 - - - +
116B VAL* 1.3 64.4 + - - +
118B GLN* 3.3 17.6 + - - -
119B ASN 3.1 16.1 + - - -
120B VAL* 3.3 30.1 + - + +
123B ILE* 3.8 15.3 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 2.8 28.8 + - + +
113B GLU* 3.9 4.5 - - - +
115B PHE* 1.3 72.3 - - - +
117B SER* 1.3 59.1 + - - +
119B ASN* 2.9 27.7 + - - -
123B ILE* 4.5 4.9 - - + -
137B GLU 4.0 12.1 - - - +
138B TRP* 3.6 38.1 - - + +
140B LYS* 3.8 27.9 + - - +
141B ILE* 4.0 21.8 - - + +
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Residues in contact with SER 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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113B GLU* 3.1 20.2 + - - -
114B THR* 3.3 8.7 + - - -
116B VAL* 1.3 77.2 - - - +
118B GLN* 1.3 61.3 + - - +
119B ASN* 3.3 5.7 + - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 2.9 35.9 + - - -
66A ILE* 3.2 31.7 - - + +
118A GLN* 2.9 50.0 + - - +
120A VAL* 4.3 4.7 - - - +
64B SER* 3.9 0.3 + - - -
66B ILE* 4.8 9.6 - - - +
114B THR* 2.9 17.1 + - + +
115B PHE* 3.6 20.5 - - - +
116B VAL 3.2 0.4 - - - -
117B SER* 1.3 74.7 - - - +
119B ASN* 1.3 69.1 + - - +
120B VAL* 3.4 9.6 + - + +
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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