Contacts of the helix formed by residues 99 - 115 (chain A) in PDB entry 3QNQ
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 ASP 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 1.3 73.4 - - - +
100A ALA* 1.3 58.9 + - - +
102A ALA* 3.3 24.8 + - + +
103A SER* 2.8 29.3 + - - -
160A TYR* 3.9 11.5 + - - +
164A VAL* 6.1 0.8 - - - +
182A ARG* 2.5 64.7 + - - +
186A ALA* 5.7 0.7 - - - +
443A ZDM 4.4 1.8 - - - +
444A CIT 3.8 18.4 + - - +
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.3 35.2 - - + +
93A GLY 4.9 0.2 - - - -
94A GLU* 4.0 30.7 - - + +
98A VAL 3.0 8.3 + - - +
99A ASP* 1.3 68.6 + - - +
101A LEU* 1.3 68.6 + - - +
102A ALA 3.0 1.3 - - - -
103A SER* 3.0 8.6 + - - -
104A GLY 2.7 23.0 + - - -
182A ARG* 5.1 0.4 - - - +
444A CIT 5.0 2.0 + - - -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.1 3.9 - - + -
90A TYR* 3.4 10.6 + - + -
99A ASP* 3.6 1.0 + - - -
100A ALA* 1.3 76.0 - - - +
102A ALA* 1.3 67.6 - - - +
104A GLY* 3.8 0.3 - - - -
105A ALA* 2.9 24.4 + - - +
182A ARG* 3.6 20.8 - - - +
443A ZDM 4.1 28.0 - - - +
31B LEU* 4.0 31.6 - - + -
86B PHE* 4.0 21.3 - - + -
87B GLY* 5.7 1.8 - - - -
90B TYR* 3.8 40.6 - - + +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP* 3.3 26.6 + - + +
100A ALA 3.0 0.2 - - - -
101A LEU* 1.3 78.5 - - - +
103A SER* 1.3 66.6 + - - +
104A GLY 2.8 1.0 + - - -
105A ALA* 2.9 6.2 + - - +
106A LEU* 2.7 26.0 + - - +
160A TYR* 3.5 20.4 - - + +
186A ALA* 4.8 0.4 - - + -
443A ZDM 3.7 34.0 - - + +
31B LEU* 5.1 0.2 - - - -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA* 3.0 23.8 + - - +
90A TYR* 3.8 0.3 - - - -
93A GLY* 3.9 6.1 - - - -
98A VAL* 4.7 0.7 - - - -
99A ASP 2.8 17.2 + - - -
100A ALA* 3.0 16.5 + - - -
102A ALA* 1.3 72.5 - - - +
104A GLY* 1.3 59.1 + - - +
106A LEU* 3.6 7.4 - - - +
107A SER* 3.1 31.9 + - - -
157A THR* 4.2 13.3 + - - +
160A TYR* 3.9 25.2 - - - -
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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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86A PHE* 3.1 33.7 - - - -
89A ALA* 4.0 3.1 - - - -
90A TYR* 4.0 18.2 - - - -
100A ALA 2.7 19.9 + - - -
101A LEU 3.8 0.7 - - - -
102A ALA 2.8 0.6 + - - -
103A SER* 1.3 71.7 + - - +
105A ALA* 1.3 61.1 + - - -
106A LEU 3.1 1.6 - - - -
107A SER* 3.5 1.2 + - - -
108A LEU* 3.3 16.3 + - - +
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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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86A PHE* 3.2 16.2 - - + -
101A LEU 2.9 15.7 + - - +
102A ALA* 2.9 3.6 + - - +
104A GLY* 1.3 74.8 - - - +
106A LEU* 1.3 62.0 + - - +
108A LEU* 3.9 8.3 - - + +
109A VAL* 3.3 26.5 + - - +
31B LEU* 4.0 32.1 - - + -
35B PHE* 3.6 10.5 - - + -
83B ILE* 4.8 5.6 - - + +
86B PHE* 6.2 0.7 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 2.7 16.3 + - - +
103A SER* 3.6 6.7 - - - +
105A ALA* 1.3 78.7 - - - +
107A SER* 1.3 58.0 + - - +
109A VAL* 3.4 2.3 + - + +
110A THR* 2.9 36.4 + - - +
156A SER* 4.1 9.0 - - - +
160A TYR* 3.8 35.4 - - + -
190A GLY* 4.0 24.2 - - - +
193A VAL* 3.9 23.6 - - + -
194A VAL* 4.5 8.1 - - + -
443A ZDM 5.0 4.7 - - + -
35B PHE* 3.7 27.1 - - + -
38B ILE* 5.4 0.2 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 4.2 8.8 - - - +
89A ALA* 3.1 36.7 - - - +
103A SER 3.1 9.4 + - - -
104A GLY 3.5 1.5 + - - -
105A ALA 3.4 0.2 - - - -
106A LEU* 1.3 73.6 - - - +
108A LEU* 1.3 60.2 + - - +
110A THR* 3.6 9.6 - - - -
111A PHE* 3.0 25.8 + - - +
152A ILE* 3.9 4.5 - - - +
153A ALA* 3.5 12.2 - - - -
156A SER* 3.5 21.6 + - - -
157A THR* 3.5 5.7 + - - -
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Residues in contact with LEU 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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82A LEU* 4.1 24.9 - - + +
85A VAL* 3.8 16.1 - - + +
86A PHE* 4.4 13.9 - - + -
104A GLY 3.3 16.4 + - - +
105A ALA* 4.0 11.4 - - - +
107A SER* 1.3 76.0 - - - +
109A VAL* 1.3 69.7 + - + +
111A PHE* 3.2 12.3 + - - +
112A LEU* 3.2 20.4 + - + +
79B ILE* 5.0 6.3 - - + -
82B LEU* 5.1 5.6 - - + -
83B ILE* 4.0 26.7 - - + +
86B PHE* 5.7 2.7 - - + -
108B LEU* 4.0 33.0 - - + -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.3 11.8 + - - +
106A LEU 3.6 8.1 - - - +
108A LEU* 1.3 81.4 - - + +
110A THR* 1.3 58.5 + - - +
112A LEU* 3.8 3.3 + - - +
113A LEU* 3.1 23.9 + - - +
194A VAL* 4.4 15.7 - - + -
35B PHE* 4.0 23.6 - - + -
75B ALA* 3.7 29.1 - - + +
76B THR* 4.4 7.9 - - + -
79B ILE* 4.7 1.1 - - + -
83B ILE* 3.2 37.2 - - + -
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Residues in contact with THR 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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106A LEU* 2.9 18.4 + - - +
107A SER 3.7 5.4 - - - -
108A LEU 3.1 0.8 - - - -
109A VAL* 1.3 77.2 - - - +
111A PHE* 1.3 63.6 + - - +
113A LEU* 3.6 8.0 + - + +
114A ALA* 3.2 21.0 + - - +
152A ILE* 3.4 17.8 - - + +
156A SER* 3.4 17.9 + - - +
193A VAL* 4.1 9.2 - - - +
194A VAL* 4.2 11.0 - - - +
197A VAL* 3.2 38.5 - - + +
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Residues in contact with PHE 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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81A ALA* 3.5 38.6 - - + -
82A LEU* 4.0 17.0 - - + -
85A VAL* 3.6 19.5 - - + -
107A SER 3.0 13.6 + - - +
108A LEU* 3.4 10.5 - - - +
110A THR* 1.3 75.8 - - - +
112A LEU* 1.3 59.7 + - + +
114A ALA* 2.8 21.8 + - + +
115A THR* 3.0 21.0 + - + -
140A LEU 4.0 8.7 - - - -
141A MET* 3.9 26.0 - - + -
145A GLY* 4.2 3.1 - - - -
148A VAL* 3.1 35.9 - - + -
149A ALA* 3.6 11.7 - - + -
152A ILE* 3.8 10.7 - - + +
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Residues in contact with LEU 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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82A LEU* 4.1 13.9 - - + -
108A LEU* 3.2 16.7 + - + +
109A VAL* 4.2 4.9 - - - +
111A PHE* 1.3 76.6 - - + +
113A LEU* 1.3 58.5 + - - +
115A THR* 2.8 30.8 - - - +
117A PHE* 3.1 17.2 - - + -
136A ILE* 4.4 15.7 - - + -
141A MET* 3.7 31.4 - - + -
75B ALA* 4.3 2.2 - - + -
79B ILE* 3.2 44.9 - - + -
82B LEU* 3.9 20.0 - - + -
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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 VAL* 3.1 19.8 + - + +
110A THR* 3.8 7.2 - - - +
111A PHE 3.1 0.8 - - - -
112A LEU* 1.3 79.7 - - - +
114A ALA* 1.3 58.1 + - - +
115A THR 3.6 0.2 + - - -
117A PHE* 5.2 0.4 - - - -
194A VAL* 4.0 24.0 - - + +
197A VAL* 4.6 5.4 - - + -
198A TRP* 3.8 39.3 - - + +
201A ARG* 3.1 32.4 + - + +
71B TYR* 3.4 33.7 - - + +
72B PRO* 3.4 20.9 - - + -
75B ALA* 3.4 10.5 - - + +
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Residues in contact with ALA 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 THR 3.2 14.0 + - - +
111A PHE* 2.8 6.7 + - + +
113A LEU* 1.3 79.1 - - - +
115A THR* 1.3 64.1 + - + +
116A PRO* 4.0 5.9 - - - +
148A VAL* 6.0 1.1 - - + -
152A ILE* 4.3 11.0 - - + -
197A VAL* 4.1 11.2 - - + -
201A ARG* 4.5 11.7 + - - +
211A SER* 5.3 0.5 - - - -
212A ILE* 3.5 48.3 + - + +
213A HIS 4.9 0.9 + - - -
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Residues in contact with THR 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 PHE* 3.0 29.2 + - + +
112A LEU* 2.8 29.8 - - - +
113A LEU 4.3 2.4 - - - +
114A ALA* 1.3 83.3 - - + +
116A PRO* 1.3 68.6 - - - +
117A PHE* 3.5 7.8 - - - -
136A ILE* 5.6 1.3 - - - +
137A PRO* 5.6 2.2 - - - +
140A LEU* 4.2 28.0 - - + +
141A MET* 3.8 19.3 - - + +
148A VAL* 5.3 4.0 - - + -
201A ARG* 5.0 0.2 + - - -
212A ILE* 6.4 0.2 - - + -
213A HIS* 4.4 17.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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