Contacts of the helix formed by residues 102 - 115 (chain A) in PDB entry 1Q0R
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLY* 4.2 4.0 - - - -
101A LEU* 1.3 86.0 - - - +
103A MET* 1.3 68.1 + - - -
105A ALA* 2.9 18.0 + - - +
106A THR* 3.8 3.3 + - - -
125A LEU 2.9 13.5 + - - -
126A LEU* 3.2 16.3 + - - +
127A GLY* 4.0 5.2 - - - -
276A HIS* 2.8 30.2 + - - -
600A AKT 3.2 28.8 - - - +
2712A 1PE 3.6 5.7 - - - -
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Residues in contact with MET 103 (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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31A GLY* 4.1 0.8 - - - -
32A GLY* 3.6 35.7 - - - +
59A HIS* 5.5 0.4 - - + -
77A PHE* 3.6 24.2 - - + -
80A LEU* 4.1 13.5 - - + -
101A LEU 3.3 0.2 + - - -
102A SER* 1.3 80.8 + - - +
104A GLY* 1.3 57.2 + - - +
106A THR* 3.1 21.1 + - - -
107A ILE* 3.2 23.0 + - + +
219A HIS* 3.9 11.7 - - + -
222A LEU* 3.6 28.3 - - + -
600A AKT 3.3 51.1 - - + +
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Residues in contact with GLY 104 (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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29A VAL* 4.0 8.7 - - - +
30A MET 3.3 20.2 + - - -
100A GLY* 3.7 0.4 - - - -
101A LEU 2.8 24.2 + - - -
103A MET* 1.3 76.7 - - - +
105A ALA* 1.3 57.7 + - - -
107A ILE* 3.3 7.2 + - - +
108A THR* 2.9 33.3 + - - +
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Residues in contact with ALA 105 (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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100A GLY 3.6 20.9 - - - +
102A SER 2.9 13.4 + - - +
104A GLY* 1.3 74.1 - - - +
106A THR* 1.3 60.5 + - - +
108A THR* 2.9 20.9 + - - -
109A GLN* 3.0 29.5 + - - +
124A MET* 3.7 19.4 - - + +
125A LEU 4.3 7.9 - - - +
127A GLY* 4.3 12.1 - - - -
128A GLY 4.9 1.6 - - - +
259A LEU* 5.1 0.4 - - + -
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Residues in contact with THR 106 (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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77A PHE* 3.6 26.2 - - + -
102A SER 4.4 2.3 + - - -
103A MET* 3.1 13.0 + - - -
105A ALA* 1.3 75.9 - - - +
107A ILE* 1.3 65.7 + - - +
109A GLN* 3.2 11.9 + - - +
110A VAL* 3.2 21.8 + - - +
128A GLY 4.4 5.0 + - - -
129A GLY 5.9 0.2 - - - -
130A LEU* 3.7 20.1 - - + +
224A LEU* 4.3 6.7 - - + -
225A PRO* 4.2 10.5 - - + -
600A AKT 3.5 30.8 + - - +
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Residues in contact with ILE 107 (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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29A VAL* 4.2 12.3 - - + -
59A HIS* 3.4 31.2 - - + +
77A PHE* 3.7 21.8 - - + -
80A LEU* 3.8 41.7 - - + +
81A ALA* 3.8 13.0 - - - +
84A ALA* 4.9 0.9 - - + -
103A MET* 3.2 14.7 + - + +
104A GLY* 3.5 18.6 - - - +
106A THR* 1.3 76.0 - - - +
108A THR* 1.3 58.2 + - - +
110A VAL* 3.1 9.6 + - - +
111A ILE* 3.0 29.7 + - + +
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Residues in contact with THR 108 (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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29A VAL* 4.1 11.0 - - + -
98A VAL* 3.6 24.7 - - + -
100A GLY* 3.4 19.1 - - - +
104A GLY 2.9 20.0 + - - +
105A ALA* 2.9 20.4 + - - -
107A ILE* 1.3 73.9 - - - +
109A GLN* 1.3 59.5 + - - +
111A ILE* 3.3 11.2 + - + +
112A ALA* 2.9 27.4 + - - +
122A LEU* 3.7 21.7 - - - +
124A MET* 3.3 14.2 - - - +
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Residues in contact with GLN 109 (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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105A ALA 3.0 28.6 + - - +
106A THR* 3.2 10.6 + - - +
108A THR* 1.3 76.0 - - - +
110A VAL* 1.3 62.6 + - - +
112A ALA* 3.2 8.7 + - - +
113A LEU* 3.1 29.1 + - - +
122A LEU* 4.9 0.4 - - - -
124A MET* 3.6 17.2 - - + -
128A GLY 2.9 24.2 + - - -
130A LEU* 3.1 43.7 + - + +
233A LEU* 3.5 18.6 - - + +
259A LEU* 3.4 25.4 - - + +
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Residues in contact with VAL 110 (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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77A PHE* 4.1 16.6 - - + +
78A GLY* 4.5 9.4 - - - +
81A ALA* 3.7 18.4 - - + -
106A THR 3.2 12.4 + - - +
107A ILE 3.1 9.4 + - - +
109A GLN* 1.3 74.2 - - - +
111A ILE* 1.3 64.7 + - - +
113A LEU* 3.2 6.8 + - - +
114A ASP* 2.9 41.7 + - + +
115A HIS* 5.7 0.4 - - + -
130A LEU* 4.6 7.4 - - + -
225A PRO* 4.0 27.4 - - + -
229A ARG* 4.2 10.8 - - - +
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Residues in contact with ILE 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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27A LEU* 5.4 0.9 - - + -
29A VAL* 4.8 1.1 - - + -
81A ALA* 3.7 19.1 - - + +
84A ALA* 3.6 28.7 - - + -
85A VAL* 4.5 7.9 - - + -
88A LEU* 6.5 0.7 - - + -
98A VAL* 4.4 13.0 - - + -
107A ILE* 3.0 24.2 + - + +
108A THR* 3.3 24.0 + - + +
110A VAL* 1.3 75.0 - - - +
112A ALA* 1.3 58.0 + - - +
115A HIS* 2.8 57.1 + - + +
118A ARG* 5.6 0.7 - - + -
119A LEU* 3.8 26.9 - - + -
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Residues in contact with ALA 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 THR 2.9 14.0 + - - +
109A GLN* 3.5 11.0 - - - +
110A VAL 3.2 0.4 - - - -
111A ILE* 1.3 76.5 - - - +
113A LEU* 1.3 59.4 + - - +
116A HIS* 3.3 28.1 - - - +
119A LEU* 3.7 15.9 - - + -
122A LEU* 3.8 21.3 - - + -
233A LEU* 4.5 3.1 - - + -
236A VAL* 4.0 25.1 - - + +
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Residues in contact with LEU 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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109A GLN 3.1 17.1 + - - +
110A VAL* 3.8 4.7 - - - +
112A ALA* 1.3 80.8 - - - +
114A ASP* 1.3 72.5 + - - +
115A HIS 3.7 0.2 - - - -
116A HIS* 4.7 4.0 + - - +
130A LEU* 3.8 21.3 - - + -
229A ARG* 3.6 46.4 - - - +
232A GLU* 3.5 40.8 - - + +
233A LEU* 3.7 15.5 - - + +
236A VAL* 4.5 3.8 - - + -
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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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78A GLY* 5.9 0.7 - - - -
110A VAL* 2.9 21.3 + - + +
113A LEU* 1.3 80.0 - - - +
115A HIS* 1.3 81.8 + - + +
116A HIS 3.8 0.9 - - - -
117A ASP* 4.7 3.0 - - - +
229A ARG* 2.8 44.8 + - - -
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Residues in contact with HIS 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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78A GLY* 5.0 2.2 - - - -
81A ALA* 4.4 5.9 - - + +
82A ALA* 4.1 33.5 - - + +
85A VAL* 3.6 36.7 - - + +
110A VAL* 4.4 1.5 + - + -
111A ILE* 2.8 31.3 + - + +
114A ASP* 1.3 93.2 + - + +
116A HIS* 1.3 62.7 + - - +
117A ASP* 3.1 12.1 - - - -
118A ARG* 3.0 22.3 + - + +
119A LEU* 4.1 5.4 - - - +
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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