Contacts of the helix formed by residues 105 - 117 (chain B) in PDB entry 1QXP
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B GLN* 3.0 25.6 - - - -
104B ASP* 1.3 91.3 + - - +
106B TRP* 1.3 68.9 + - - +
107B LEU* 3.2 2.7 - - - +
108B LEU* 3.0 26.9 - - - +
109B ALA* 4.0 2.6 + - - +
261B GLY* 4.1 27.2 + - - +
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Residues in contact with TRP 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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104B ASP* 4.2 24.1 + - + +
105B SER* 1.3 80.9 + - - +
107B LEU* 1.3 113.4 + - + +
108B LEU 3.5 0.2 + - - -
109B ALA* 3.7 5.5 + - - +
110B ALA* 4.5 0.5 + - - +
185B TYR* 4.2 3.8 - + - -
195B LEU* 2.8 44.4 - - + -
196B SER* 4.2 1.9 - - - +
197B GLY* 3.4 18.3 - - - +
198B GLY* 3.1 39.2 + - - +
199B CYS 3.4 17.7 - - - -
200B THR* 3.1 37.3 + - + +
203B ALA* 3.9 6.3 - - + -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP 5.2 1.5 - - - +
105B SER* 3.2 2.1 - - - +
106B TRP* 1.3 117.7 - - + +
108B LEU* 1.3 64.3 + - - +
109B ALA 3.3 0.9 - - - -
110B ALA* 3.1 5.9 - - + +
111B ILE* 3.1 42.1 + - + +
168B VAL* 4.3 12.6 - - + -
182B GLU* 4.2 27.8 - - + +
185B TYR* 3.4 26.9 - - + -
195B LEU* 5.3 3.1 - - + -
203B ALA* 3.6 10.8 - - + -
207B PHE* 4.3 5.4 - - + -
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Residues in contact with LEU 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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97B ILE* 2.9 33.7 - - + -
98B CYS* 4.1 4.3 - - - +
99B GLN* 3.9 42.0 - - + +
105B SER* 3.0 22.6 - - - +
107B LEU* 1.3 78.8 - - - +
109B ALA* 1.4 60.2 + - - +
111B ILE* 3.9 0.9 - - + -
112B ALA* 3.2 25.1 + - - +
168B VAL* 4.5 13.0 - - + +
261B GLY 4.7 9.2 - - - +
262B HIS* 4.2 26.2 - - + +
288B TRP* 4.2 9.4 - - + -
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Residues in contact with ALA 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 SER 4.0 2.5 + - - +
106B TRP* 3.7 4.7 + - - +
107B LEU 3.3 1.2 - - - -
108B LEU* 1.4 77.4 - - - +
110B ALA* 1.3 54.3 + - - +
112B ALA* 3.5 3.3 + - - +
113B SER* 2.7 37.8 + - - -
200B THR* 3.8 18.8 - - + +
204B PHE* 3.8 8.6 - - + -
261B GLY 5.3 2.8 + - - +
262B HIS 4.9 3.8 - - - +
263B ALA* 4.3 25.0 - - + +
288B TRP* 5.3 2.7 - - - -
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Residues in contact with ALA 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 TRP 4.5 1.3 + - - +
107B LEU* 3.1 14.6 - - - +
109B ALA* 1.3 77.3 - - - +
111B ILE* 1.3 70.4 + - - +
113B SER* 3.3 2.9 + - - -
114B LEU* 3.0 24.4 + - - +
200B THR* 4.6 4.9 + - - +
203B ALA* 3.8 18.2 - - + -
204B PHE* 3.5 19.2 - - + -
207B PHE* 3.6 26.0 - - + -
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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
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97B ILE* 4.3 13.7 - - + -
107B LEU* 3.1 38.5 + - + +
108B LEU* 4.2 4.3 - - - +
110B ALA* 1.3 86.1 - - - +
112B ALA* 1.3 66.3 + - - +
114B LEU* 3.2 22.0 + - - +
115B THR* 3.7 6.8 + - - -
168B VAL* 4.2 15.3 - - + -
177B TRP* 4.0 25.5 - - + -
178B SER* 3.9 27.4 - - - +
181B LEU* 4.2 12.6 - - + -
182B GLU 5.1 1.1 - - - +
207B PHE* 4.3 8.5 - - + -
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Residues in contact with ALA 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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95B THR* 4.3 5.8 - - + -
97B ILE* 4.3 7.8 - - + +
108B LEU 3.2 18.4 + - - +
109B ALA* 3.8 2.7 - - - +
110B ALA 3.1 0.2 - - - -
111B ILE* 1.3 80.4 - - - +
113B SER* 1.4 61.6 + - - +
114B LEU 3.1 1.1 - - - -
115B THR* 2.7 31.5 + - - -
116B LEU* 3.3 10.8 - - - +
287B PRO* 4.0 12.9 - - + +
288B TRP* 3.7 28.7 - - + -
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Residues in contact with SER 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 ALA 2.7 23.5 + - - -
110B ALA 3.5 0.2 - - - -
112B ALA* 1.4 68.1 - - - +
114B LEU* 1.4 61.9 + - - +
115B THR 2.6 15.9 + - - -
116B LEU* 2.9 32.1 + - - +
117B ASN* 3.6 5.4 + - - +
204B PHE* 2.8 35.8 - - - -
237B LEU* 4.1 16.5 - - - +
265B SER* 5.1 5.6 - - - -
287B PRO* 4.9 0.6 - - - +
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Residues in contact with LEU 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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110B ALA 3.0 12.2 + - - +
111B ILE* 3.4 12.8 - - - +
112B ALA 3.1 0.6 - - - -
113B SER* 1.4 87.0 + - - +
115B THR* 1.4 58.8 + - - +
117B ASN 3.5 7.8 - - - +
120B ILE* 3.6 29.4 - - + +
121B LEU* 3.0 34.9 - - + +
124B VAL* 4.1 15.9 - - + -
125B VAL* 6.4 0.7 - - + -
177B TRP* 5.1 6.7 - - + -
181B LEU* 4.7 10.5 - - + -
204B PHE* 5.0 2.2 - - + -
207B PHE* 3.8 41.3 - - + +
208B THR* 4.3 6.7 - - - +
237B LEU* 5.0 1.3 - - + -
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Residues in contact with THR 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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90B ASP* 5.0 14.9 + - - +
92B ALA 5.3 2.7 - - - +
93B THR* 5.0 6.7 - - - +
94B ARG 4.5 11.4 - - - +
95B THR* 4.4 23.3 + - + -
111B ILE 3.7 9.5 + - - -
112B ALA* 2.7 19.1 + - - -
113B SER 2.6 6.9 - - - -
114B LEU* 1.4 71.6 - - - +
116B LEU* 1.2 75.3 + - - +
117B ASN* 3.0 6.5 + - - -
118B GLU* 4.2 10.2 + - - +
121B LEU* 4.3 5.4 - - - +
177B TRP* 4.0 18.0 - - - -
285B ARG* 5.7 1.8 + - - +
287B PRO* 5.4 4.5 - - + +
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Residues in contact with LEU 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 ALA 3.3 23.8 - - - +
113B SER* 3.3 18.2 - - - +
115B THR* 1.2 88.2 - - + +
117B ASN* 1.3 58.9 + - + +
118B GLU 4.0 1.2 + - - -
265B SER* 3.3 32.1 - - - +
267B THR* 4.3 14.4 - - + -
285B ARG* 4.0 49.9 + - + +
287B PRO* 3.3 26.2 - - + -
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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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113B SER 3.6 6.4 + - - +
114B LEU 3.5 4.9 - - - +
115B THR 3.1 3.5 - - - -
116B LEU* 1.3 81.3 - - + +
118B GLU* 1.3 65.7 + - - +
119B THR* 3.3 8.2 + - - -
120B ILE* 2.6 63.3 + - + +
121B LEU* 2.9 24.1 + - - +
235B GLY 5.4 1.8 + - - -
237B LEU* 4.8 9.2 - - + +
347B ALA* 6.0 3.4 - - - +
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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