Contacts of the helix formed by residues 99 - 115 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600C ZDM 4.5 2.4 - - - +
98D VAL* 1.3 74.2 - - - +
100D ALA* 1.3 59.0 + - - +
101D LEU 3.6 0.2 + - - -
102D ALA* 3.3 19.3 + - - +
103D SER* 2.9 28.8 + - - -
160D TYR* 3.5 17.4 + - - +
164D VAL* 6.0 1.0 - - - +
182D ARG* 2.7 59.6 + - - +
186D ALA* 5.5 1.2 - - - +
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D TYR* 3.3 44.4 - - + +
93D GLY* 4.6 1.1 - - - -
94D GLU* 4.1 15.9 - - + +
98D VAL 3.0 7.8 + - - +
99D ASP* 1.3 67.9 + - - +
101D LEU* 1.3 70.2 + - - +
102D ALA 2.8 2.1 + - - -
103D SER* 3.0 9.5 + - - -
104D GLY 2.8 22.0 + - - -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.1 28.7 - - + -
86C PHE* 3.7 28.5 - - + -
87C GLY* 5.6 2.0 - - - -
90C TYR* 3.6 45.1 + - + +
600C ZDM 4.3 17.3 - - + -
86D PHE* 4.2 2.5 - - + -
90D TYR* 3.4 9.5 - - + -
99D ASP* 3.6 1.2 + - - -
100D ALA* 1.3 76.6 - - - +
102D ALA* 1.3 65.8 + - - +
104D GLY* 3.4 1.0 + - - -
105D ALA* 3.1 19.2 + - - +
182D ARG* 3.5 25.9 - - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.1 0.2 - - - -
600C ZDM 3.7 33.9 - - + +
99D ASP* 3.3 25.9 + - - +
100D ALA 2.8 1.0 + - - -
101D LEU* 1.3 74.1 - - - +
103D SER* 1.3 55.1 + - - +
104D GLY 2.7 15.4 + - - -
105D ALA* 2.7 16.1 + - - +
106D LEU* 2.8 14.4 + - - +
160D TYR* 3.4 21.8 - - + +
186D ALA* 4.7 0.2 - - + -
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Residues in contact with SER 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 2.9 31.6 + - - +
93D GLY* 3.5 13.6 - - - -
99D ASP 2.9 11.2 + - - -
100D ALA* 3.3 6.8 + - - -
102D ALA* 1.3 76.4 - - - +
104D GLY* 1.3 59.5 + - - +
106D LEU* 4.0 10.5 - - - +
107D SER* 3.5 12.1 + - - -
157D THR* 3.5 26.3 + - - +
160D TYR* 3.6 23.5 - - - -
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PHE* 2.8 38.1 - - - -
89D ALA* 3.5 13.7 - - - +
90D TYR* 3.5 15.5 - - - -
100D ALA 2.8 13.5 + - - -
101D LEU 3.8 0.9 - - - -
102D ALA 2.7 4.9 + - - -
103D SER* 1.3 74.9 + - - +
105D ALA* 1.3 58.6 + - - +
107D SER 4.1 1.3 + - - -
108D LEU 3.8 6.8 + - - -
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.2 26.9 - - + -
35C PHE* 4.1 11.4 - - + -
83C ILE* 5.1 4.5 - - + -
86D PHE* 3.8 14.8 - - + -
101D LEU 3.1 14.0 + - - +
102D ALA 2.7 6.3 + - - +
104D GLY* 1.3 71.9 - - - -
106D LEU* 1.3 66.2 + - - +
107D SER 3.2 1.8 - - - -
108D LEU* 3.3 10.1 + - + +
109D VAL* 3.0 26.5 + - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.7 28.8 - - + -
600C ZDM 5.0 6.3 - - + -
102D ALA 2.8 14.9 + - - +
103D SER* 4.0 9.0 - - - +
105D ALA* 1.3 78.6 - - - +
107D SER* 1.3 52.6 + - - +
109D VAL* 3.2 3.6 + - - +
110D THR* 2.8 37.9 + - - +
156D SER* 4.1 9.6 - - - +
160D TYR* 4.4 20.0 - - + -
190D GLY* 3.7 28.7 - - - +
193D VAL* 3.3 41.5 - - + -
194D VAL* 4.6 6.1 - - + -
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 3.3 22.9 - - - -
89D ALA* 3.2 29.2 - - - +
103D SER 3.5 3.8 + - - -
104D GLY 4.3 1.3 - - - -
105D ALA 3.2 0.6 - - - -
106D LEU* 1.3 79.5 - - - +
108D LEU* 1.3 53.4 + - - +
110D THR* 3.5 8.1 - - - -
111D PHE* 2.6 36.9 + - - +
152D ILE* 3.6 2.5 - - - +
153D ALA* 3.2 19.4 + - - -
156D SER* 3.5 13.3 - - - -
157D THR* 3.8 0.2 + - - -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 5.6 1.6 - - + -
82C LEU* 4.6 15.9 - - + -
83C ILE* 4.5 26.2 - - + -
86C PHE* 6.4 0.9 - - + -
108C LEU* 3.9 36.3 - - + -
82D LEU* 4.0 28.9 - - + +
85D VAL* 3.9 5.3 - - - +
86D PHE* 4.4 15.7 - - + +
104D GLY 3.8 11.3 + - - +
105D ALA* 3.3 16.6 + - + +
107D SER* 1.3 79.0 - - - +
109D VAL* 1.3 65.0 + - + +
111D PHE* 3.7 6.5 - - - +
112D LEU* 3.4 22.3 + - + +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.8 23.1 - - + -
75C ALA* 3.8 30.6 - - + +
76C THR* 4.5 5.4 - - + -
79C ILE* 5.1 2.5 - - + -
83C ILE* 3.8 32.3 - - + -
105D ALA 3.0 16.1 + - - +
106D LEU 3.5 7.2 - - - +
108D LEU* 1.3 73.4 - - + +
110D THR* 1.3 71.6 + - - +
111D PHE 3.0 1.1 - - - -
112D LEU* 2.8 18.7 + - - +
113D LEU* 2.9 10.4 + - + -
194D VAL* 4.3 20.9 - - + -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 2.8 25.6 + - - +
107D SER* 3.5 2.5 - - - -
109D VAL* 1.3 74.4 - - - +
111D PHE* 1.3 65.0 + - - +
113D LEU* 3.2 11.5 + - - +
114D ALA* 3.0 18.4 + - - +
152D ILE* 3.3 22.7 - - + -
156D SER* 3.1 21.8 + - - +
193D VAL* 4.6 0.2 - - - +
194D VAL* 4.5 14.5 + - - +
197D VAL* 3.3 37.1 - - + +
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Residues in contact with PHE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ALA* 3.8 32.5 - - + -
82D LEU* 3.5 26.2 - - + -
85D VAL* 4.0 11.7 - - + -
107D SER 2.6 21.6 + - - +
108D LEU* 3.7 9.0 - - - +
109D VAL 2.9 0.6 + - - -
110D THR* 1.3 73.1 - - - +
112D LEU* 1.3 58.4 + - + +
114D ALA* 2.9 20.4 + - - +
115D THR* 3.1 15.6 + - + +
140D LEU 3.9 11.7 - - - -
141D MET* 3.6 24.2 - - + -
145D GLY* 4.5 2.5 - - - -
148D VAL* 3.3 28.5 - - + -
149D ALA* 3.7 12.8 - - - -
152D ILE* 3.3 24.2 - - + -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ALA* 4.2 4.7 - - + -
79C ILE* 2.8 35.0 - - + -
82C LEU* 3.7 16.2 - - + -
82D LEU* 4.1 14.1 - - + -
108D LEU 3.4 15.3 - - - +
109D VAL* 2.8 11.0 + - - +
111D PHE* 1.3 72.9 - - - +
113D LEU* 1.3 57.6 + - - +
115D THR* 2.9 16.5 - - - +
117D PHE* 2.9 38.1 - - + -
136D ILE* 4.5 14.1 - - + -
141D MET* 3.6 39.3 - - + -
201D ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.7 10.8 - - + -
72C PRO* 3.4 41.7 - - + -
75C ALA* 3.7 16.3 - - + +
109D VAL* 2.9 10.9 + - + +
110D THR* 3.3 11.7 - - - +
111D PHE 3.1 0.2 - - - -
112D LEU* 1.3 79.3 - - - +
114D ALA* 1.3 58.8 + - - +
115D THR 3.2 1.1 + - - +
194D VAL* 3.3 34.5 - - + +
197D VAL* 3.4 20.0 - - + -
198D TRP* 3.4 15.5 - - + +
201D ARG* 3.2 30.8 + - - +
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D THR 3.0 11.4 + - - +
111D PHE* 2.9 10.5 + - - +
113D LEU* 1.3 75.1 - - - +
115D THR* 1.3 64.3 + - + +
116D PRO* 3.8 6.7 - - - +
148D VAL* 5.3 2.2 - - + -
152D ILE* 4.5 12.6 - - + -
197D VAL* 4.2 9.9 - - + -
201D ARG* 4.7 11.3 + - - +
211D SER* 5.1 0.5 + - - -
212D ILE* 3.6 48.3 + - + +
213D HIS 4.8 1.0 + - - -
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 3.1 27.8 + - + +
112D LEU* 2.9 26.2 - - - +
113D LEU 3.2 1.3 - - - +
114D ALA* 1.3 82.9 - - - +
116D PRO* 1.4 60.9 - - + +
117D PHE* 3.0 22.8 + - - -
136D ILE* 5.7 1.0 - - - +
137D PRO* 5.4 3.5 - - - +
140D LEU* 4.3 25.4 - - + +
141D MET* 3.7 20.6 - - + +
148D VAL* 4.8 7.0 - - + -
201D ARG* 4.3 3.0 + - - -
213D HIS* 4.6 11.9 - - + +
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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
------------------------------------------------------------
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