Contacts of the helix formed by residues 110 - 125 (chain A) in PDB entry 1QIB
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 PRO 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.1 30.1 - - + -
108A LEU 3.5 4.0 - - - +
109A ASP* 1.3 94.8 - - - +
111A GLU* 1.3 58.1 + - - +
113A VAL* 3.4 3.1 + - + +
114A ASP* 3.1 34.6 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 2.7 22.6 + - - +
110A PRO* 1.3 76.2 - - - +
112A THR* 1.3 58.6 + - - +
114A ASP* 3.5 9.7 + - - +
115A ASP* 3.2 20.8 + - + +
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.2 19.3 - - + -
109A ASP* 2.8 29.1 + - - +
111A GLU* 1.3 73.7 - - - +
113A VAL* 1.3 60.7 + - - +
115A ASP* 3.2 6.9 + - + +
116A ALA* 2.9 27.2 + - - +
119A ARG* 5.2 1.2 + - - +
188A LEU* 4.0 31.9 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.0 24.0 - - + -
105A THR* 4.4 11.2 - - + +
108A LEU* 3.8 28.9 - - + +
109A ASP 3.1 17.8 + - - +
110A PRO* 3.6 9.2 - - + +
112A THR* 1.3 77.4 - - - +
114A ASP* 1.3 62.0 + - - +
115A ASP 3.2 0.2 + - - -
116A ALA* 3.2 6.4 + - - +
117A PHE* 3.1 58.4 + - + -
146A PHE* 4.9 6.5 - - + -
195A LEU* 4.2 9.0 - - + -
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 5.3 1.6 + - - -
101A ILE* 3.2 18.0 - - - +
104A TYR* 2.7 28.4 + - - -
110A PRO* 3.1 17.9 + - - +
111A GLU* 3.7 10.1 - - + +
112A THR 3.3 0.2 - - - -
113A VAL* 1.3 74.9 - - - +
115A ASP* 1.3 56.2 + - - +
117A PHE* 3.6 2.1 + - - +
118A ALA* 3.2 28.2 + - - +
134A ARG* 3.2 36.7 + - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 3.2 12.3 + - + +
112A THR* 3.2 12.3 + - + +
113A VAL 3.1 0.6 - - - -
114A ASP* 1.3 76.6 - - - +
116A ALA* 1.3 59.5 + - - +
117A PHE 3.1 1.6 - - - -
118A ALA* 4.0 5.7 - - - +
119A ARG* 3.0 60.8 + - - +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 5.9 0.4 - - + -
112A THR* 2.9 17.4 + - + +
113A VAL* 3.2 4.7 + - - +
115A ASP* 1.3 76.9 - - - +
117A PHE* 1.3 62.3 + - - +
119A ARG* 3.4 18.8 - - - +
120A ALA* 3.4 21.5 + - - +
188A LEU* 4.4 11.2 - - + -
195A LEU* 4.6 14.6 - - + -
196A PHE* 3.7 30.8 - - + +
199A ALA* 4.8 0.2 - - - +
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 5.4 3.6 - - + -
101A ILE* 3.8 29.6 - - + -
113A VAL* 3.1 45.0 + - + +
114A ASP 3.9 5.2 - - - +
116A ALA* 1.3 77.3 - - - +
118A ALA* 1.3 63.9 + - - +
120A ALA* 3.4 4.8 + - - +
121A PHE* 3.3 32.1 + - + -
144A ILE* 3.6 26.7 - - + -
146A PHE* 4.0 20.2 - + - -
180A PHE* 3.8 28.5 - + - -
195A LEU* 4.2 12.8 - - + -
199A ALA* 3.9 15.5 - - + -
203A PHE* 3.8 13.8 - + + -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 4.3 17.6 + - - +
114A ASP 3.2 18.3 + - - +
115A ASP* 4.0 7.0 - - - +
117A PHE* 1.3 73.6 - - - +
119A ARG* 1.3 66.5 + - + +
121A PHE* 3.1 17.6 + - - +
122A GLN* 3.2 13.6 + - - +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 5.2 1.0 + - - +
115A ASP* 3.0 43.8 + - - +
116A ALA* 3.4 24.4 - - - +
118A ALA* 1.3 78.4 - - + +
120A ALA* 1.3 61.2 + - - +
122A GLN* 3.5 22.8 + - - +
123A VAL* 3.3 20.3 + - - +
188A LEU* 4.6 13.5 - - - +
196A PHE* 3.5 45.6 - - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ALA 3.4 17.4 + - - +
117A PHE 3.5 7.2 - - - +
118A ALA 3.1 0.6 - - - -
119A ARG* 1.3 79.4 - - - +
121A PHE* 1.3 56.8 + - - +
123A VAL* 2.9 26.2 - - - +
124A TRP* 3.7 7.6 + - - -
196A PHE* 3.6 13.0 - - - +
199A ALA* 3.8 5.6 - - + -
200A ALA* 3.7 23.5 - - - +
203A PHE* 3.7 19.6 - - + -
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.4 58.1 - + + -
117A PHE* 3.3 19.6 + - + -
118A ALA* 3.1 9.5 + - - +
120A ALA* 1.3 77.6 - - - +
122A GLN* 1.3 64.3 + - - +
124A TRP* 3.2 14.5 + + - +
125A SER* 3.2 10.1 + - - -
132A PHE* 3.5 57.2 - + + -
142A ILE* 4.4 16.4 - - + -
144A ILE* 5.0 1.6 - - + -
203A PHE* 3.8 45.8 - + + -
207A MET* 5.5 0.9 - - - -
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Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA 3.2 8.5 + - - +
119A ARG* 3.7 21.5 - - - +
120A ALA 3.4 0.2 - - - -
121A PHE* 1.3 75.8 - - - +
123A VAL* 1.3 65.0 + - + +
124A TRP 3.0 2.5 - - - -
125A SER* 3.1 12.6 - - - +
126A ASP* 3.0 50.8 + - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG 3.3 16.2 - - - +
120A ALA 2.9 23.1 - - - +
122A GLN* 1.3 77.1 - - - +
124A TRP* 1.3 79.3 + - + +
126A ASP* 4.3 9.0 + - - +
127A VAL* 3.9 6.6 - - - +
196A PHE* 4.1 21.8 - - + -
200A ALA* 4.2 11.9 - - + -
218A LEU* 5.1 1.6 - - + -
232A PHE* 4.2 20.9 - - + -
234A LEU* 3.4 24.9 - - + +
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA 3.7 14.8 + - - -
121A PHE* 3.2 11.1 + + - +
122A GLN 3.0 0.6 - - - -
123A VAL* 1.3 85.1 - - + +
125A SER* 1.3 57.7 + - - +
126A ASP 3.2 2.8 + - - -
127A VAL* 3.4 7.0 + - - +
128A THR* 2.7 32.6 + - - +
130A LEU* 5.4 3.6 - - + -
132A PHE* 4.7 11.7 - + + -
200A ALA 3.1 29.0 + - - -
203A PHE* 3.9 16.3 - - + -
204A GLY* 3.7 22.7 - - - +
207A MET* 5.6 4.0 - - + -
209A LEU* 3.8 23.8 - - + -
218A LEU* 3.6 20.9 - - + -
219A MET* 4.6 5.6 - - + -
234A LEU* 4.1 24.9 - - + -
238A ASP* 4.3 11.9 - - + -
242A ILE* 4.0 34.3 - - + -
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE 3.2 6.2 + - - -
122A GLN* 3.1 27.5 + - - +
124A TRP* 1.3 76.5 - - - +
126A ASP* 1.3 61.5 + - - +
127A VAL 3.3 0.4 - - - -
128A THR* 3.0 24.6 - - - +
130A LEU* 3.6 22.1 - - - +
131A ARG* 5.4 10.3 + - - -
132A PHE* 4.2 14.4 - - - -
249A SER* 4.8 1.9 + - - -
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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