Contacts of the helix formed by residues 107 - 120 (chain A) in PDB entry 1QHP
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 TRP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.3 6.3 - - + -
98A LYS 2.9 25.0 + - - -
99A GLN* 3.9 12.6 - - + +
100A ILE* 3.6 26.3 - - + +
106A ASN* 1.3 76.3 - - - +
108A THR* 1.3 57.3 + - - +
110A PHE* 3.3 27.1 + + - +
111A ASP* 2.9 36.7 + - - +
152A ASN* 6.1 0.4 - - - -
216A GLN* 3.4 39.8 + - + -
217A LEU* 3.7 25.1 - - + -
220A HIS* 3.5 46.7 - + + -
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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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106A ASN* 3.0 15.0 + - - -
107A TRP* 1.3 77.7 - - - +
109A THR* 1.4 57.5 + - - +
111A ASP* 3.3 8.5 + - + +
112A THR* 2.8 42.2 + - - +
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Residues in contact with THR 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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51A LEU* 4.0 9.2 - - + -
52A GLU* 3.9 39.5 - - + +
55A ARG* 5.8 0.2 - - - -
104A PHE 4.3 0.4 - - - +
105A GLY* 3.5 11.9 - - - -
106A ASN* 2.9 33.7 + - - -
108A THR* 1.4 76.5 - - - +
110A PHE* 1.3 64.1 + - - +
112A THR* 3.4 6.4 + - - -
113A LEU* 3.0 23.7 + - - +
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Residues in contact with PHE 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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51A LEU* 4.1 20.6 - - + +
71A LEU* 4.4 6.1 - - + -
74A VAL* 4.3 12.3 - - + -
100A ILE* 4.1 20.2 - - + -
106A ASN 3.0 11.5 + - - +
107A TRP* 3.7 25.6 - + + +
109A THR* 1.3 77.5 - - - +
111A ASP* 1.3 70.6 + - - +
113A LEU* 3.3 4.9 + - + +
114A VAL* 3.0 51.4 + - + +
124A VAL* 5.2 0.2 - - + -
126A VAL* 4.0 24.0 - - + -
217A LEU* 3.9 27.1 - - + -
220A HIS* 3.8 21.3 - - + -
222A ALA* 4.6 3.4 - - + -
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Residues in contact with ASP 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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107A TRP* 2.9 22.6 + - - +
108A THR* 3.6 7.9 - - + +
110A PHE* 1.3 77.6 - - - +
112A THR* 1.3 58.1 + - - +
114A VAL* 3.3 1.5 + - - +
115A ASN* 2.8 44.4 + - - +
220A HIS* 2.6 53.7 + - - +
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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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52A GLU* 5.2 2.7 - - - +
55A ARG* 3.6 22.2 - - - +
108A THR* 2.8 27.3 + - - +
109A THR* 3.8 6.7 - - - -
111A ASP* 1.3 76.0 - - - +
113A LEU* 1.3 63.6 + - - +
115A ASN* 3.4 4.6 + - - +
116A ASP* 2.9 34.4 + - - +
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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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51A LEU* 3.8 41.7 - - + +
54A VAL* 3.7 19.3 - - + -
55A ARG* 3.6 41.6 - - + +
58A LEU* 4.5 9.2 - - + -
69A ILE* 5.3 2.5 - - + -
71A LEU* 3.8 19.3 - - + -
109A THR 3.0 16.8 + - - +
110A PHE* 3.7 5.4 - - + +
112A THR* 1.3 78.3 - - - +
114A VAL* 1.3 61.9 + - + +
116A ASP* 3.3 1.2 + - - +
117A ALA* 2.8 28.9 + - + +
124A VAL* 5.1 4.5 - - + -
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Residues in contact with VAL 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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110A PHE* 3.0 50.7 + - + +
111A ASP 3.9 2.7 - - - +
113A LEU* 1.3 80.2 - - + +
115A ASN* 1.3 60.8 + - - +
117A ALA* 3.3 6.6 + - - +
118A HIS* 2.9 56.3 + - + +
124A VAL* 4.2 22.7 - - + -
220A HIS 4.1 5.2 - - - +
221A GLY* 3.6 23.1 - - - +
222A ALA 5.1 0.7 - - - +
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Residues in contact with ASN 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 ASP* 2.8 34.3 + - - +
112A THR* 3.9 4.7 - - - +
114A VAL* 1.3 75.3 - - - +
116A ASP* 1.3 63.1 + - - +
118A HIS* 3.4 14.1 + - - +
119A GLN* 3.0 35.5 + - - +
220A HIS 5.7 2.4 + - - -
221A GLY* 6.1 1.2 - - - -
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Residues in contact with ASP 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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55A ARG* 3.1 34.7 + - + +
58A LEU* 3.6 17.7 - - + -
112A THR* 2.9 28.4 + - - +
115A ASN* 1.3 77.1 - - - +
117A ALA* 1.3 66.0 + - - +
119A GLN* 3.2 26.0 + - - +
120A ASN* 2.9 29.6 + - - +
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Residues in contact with ALA 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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58A LEU* 3.5 24.7 - - + +
69A ILE* 4.8 1.6 - - + -
113A LEU* 2.8 19.6 + - + +
114A VAL 3.6 4.7 - - - +
116A ASP* 1.3 75.7 - - - +
118A HIS* 1.3 57.9 + - - +
120A ASN* 2.9 19.7 + - - +
121A GLY 3.2 0.2 + - - -
122A ILE* 2.9 35.0 + - + +
124A VAL* 3.8 20.4 - - + -
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Residues in contact with HIS 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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114A VAL* 2.9 34.7 + - + +
115A ASN* 3.6 13.4 + - - +
117A ALA* 1.3 76.4 - - + +
119A GLN* 1.3 62.3 + - - +
121A GLY* 3.0 13.7 + - - -
122A ILE 3.4 17.0 - - - +
123A LYS* 4.2 4.5 - - + -
124A VAL 4.5 0.6 + - - -
221A GLY* 3.2 26.2 + - - -
223A ASP* 2.7 32.7 + - - -
249A LYS* 5.8 3.6 - - - -
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Residues in contact with GLN 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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115A ASN* 3.0 21.8 + - - +
116A ASP* 3.2 34.0 + - - +
118A HIS* 1.3 76.7 - - - +
120A ASN* 1.3 61.7 + - - +
121A GLY 3.3 1.5 + - - -
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Residues in contact with ASN 120 (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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58A LEU* 4.0 23.2 - - + +
59A PRO* 5.5 4.0 - - - +
62A LYS* 2.8 48.3 + - + +
116A ASP* 2.9 24.7 + - - +
117A ALA* 2.9 10.0 + - - +
119A GLN* 1.3 79.5 - - - +
121A GLY* 1.3 60.9 + - - +
122A ILE* 3.3 18.3 + - + +
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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