Contacts of the helix formed by residues 99 - 115 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ZDM 4.8 1.8 - - - +
98B VAL* 1.3 74.9 - - - +
100B ALA* 1.3 58.9 + - - +
101B LEU* 3.6 0.3 + - - +
102B ALA* 3.4 20.5 + - + +
103B SER* 2.9 27.7 + - - -
160B TYR* 3.7 19.7 + - - +
182B ARG* 2.6 61.8 + - - +
186B ALA* 5.8 1.0 - - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.3 45.7 - - + +
93B GLY* 4.7 0.4 - - - -
94B GLU* 3.9 19.5 - - + +
98B VAL 3.1 6.5 + - - +
99B ASP* 1.3 68.8 + - - +
101B LEU* 1.3 68.3 + - - +
102B ALA 2.9 1.9 + - - -
103B SER* 2.9 8.2 + - - -
104B GLY 2.8 22.3 + - - -
182B ARG* 5.2 0.2 - - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.1 27.5 - - + +
86A PHE* 4.0 21.3 - - + -
87A GLY* 5.8 2.2 - - - -
90A TYR* 3.5 48.2 - - + +
600A ZDM 4.2 19.1 - - + -
86B PHE* 4.3 2.2 - - + -
90B TYR* 3.5 8.9 - - + -
99B ASP* 3.6 0.2 + - - -
100B ALA* 1.3 77.6 - - - +
102B ALA* 1.3 60.9 + - - +
104B GLY 3.9 0.9 - - - -
105B ALA* 3.2 22.5 + - - +
182B ARG* 3.5 26.8 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.1 0.2 - - - -
600A ZDM 3.5 34.6 - - + +
99B ASP* 3.4 20.1 + - - +
100B ALA 2.9 1.0 + - - -
101B LEU* 1.3 75.5 - - - +
103B SER* 1.3 58.3 + - - +
104B GLY 3.0 1.8 - - - -
105B ALA* 2.9 3.9 + - - +
106B LEU* 2.7 37.3 + - - +
160B TYR* 3.5 24.9 - - + +
186B ALA* 4.8 0.4 - - + -
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 2.8 28.1 + - - +
90B TYR* 3.7 0.3 - - - -
93B GLY* 3.5 10.7 - - - -
98B VAL* 4.5 0.7 - - - -
99B ASP 2.9 19.7 + - - -
100B ALA 2.9 5.0 + - - -
102B ALA* 1.3 74.2 - - - +
104B GLY* 1.3 58.1 + - - +
106B LEU* 3.8 6.0 + - - +
107B SER* 3.2 29.6 + - - -
157B THR* 3.6 21.9 + - - -
160B TYR* 3.8 20.3 - - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 2.7 49.5 - - - -
89B ALA* 3.9 3.6 - - - -
90B TYR* 3.7 20.2 - - - -
100B ALA 2.8 14.3 + - - -
101B LEU 4.1 0.7 - - - -
103B SER* 1.3 78.3 + - - +
105B ALA* 1.3 53.6 + - - +
107B SER 4.2 2.0 - - - -
108B LEU 3.9 5.9 + - - -
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.3 22.9 - - + -
35A PHE* 4.0 15.3 - - + -
83A ILE* 5.3 5.8 - - + +
86B PHE* 3.9 11.0 - - + -
101B LEU 3.2 15.7 + - - +
102B ALA* 2.9 2.9 + - - +
104B GLY* 1.3 74.6 - - - +
106B LEU* 1.3 68.7 + - - +
107B SER 3.0 1.3 - - - -
108B LEU* 3.0 8.8 + - + +
109B VAL* 2.9 25.6 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.0 24.5 - - + -
38A ILE* 5.4 0.2 - - + -
600A ZDM 5.6 4.9 - - + -
102B ALA 2.7 18.3 + - - +
103B SER* 3.8 6.5 - - - +
105B ALA* 1.3 77.3 - - - +
107B SER* 1.3 50.1 + - - +
109B VAL* 3.3 3.6 + - - +
110B THR* 2.6 40.9 + - - +
156B SER* 4.3 8.3 - - - -
160B TYR* 4.0 24.2 - - + -
190B GLY* 3.7 30.3 - - - +
193B VAL* 3.5 37.5 - - + -
194B VAL* 4.6 8.5 - - + -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.7 14.1 - - - +
89B ALA* 3.2 32.9 - - - +
103B SER 3.2 6.4 + - - -
104B GLY 4.8 0.9 - - - -
105B ALA 3.0 0.6 - - - -
106B LEU* 1.3 74.3 - - - +
108B LEU* 1.3 60.8 + - - +
110B THR* 3.7 8.5 - - - -
111B PHE* 2.9 29.3 + - - +
152B ILE* 3.7 1.5 - - - +
153B ALA* 3.7 14.6 - - - -
156B SER* 3.5 20.7 - - - -
157B THR* 3.5 2.3 + - - -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 5.8 0.2 - - + -
82A LEU* 4.5 24.0 - - + +
83A ILE* 4.7 14.4 - - + -
86A PHE* 5.8 2.9 - - + -
108A LEU* 4.0 24.2 - - + -
82B LEU* 3.5 41.5 - - + +
85B VAL* 4.0 14.7 - - + +
86B PHE* 4.7 14.6 - - + -
104B GLY 3.9 11.2 + - - +
105B ALA* 3.0 15.8 + - + +
107B SER* 1.3 79.6 - - - +
109B VAL* 1.3 63.3 + - + +
111B PHE* 3.4 2.9 - - - +
112B LEU* 3.2 26.7 + - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.6 26.5 - - + -
75A ALA* 3.7 28.4 - - + +
76A THR* 4.6 4.9 - - + -
79A ILE* 5.3 1.1 - - + -
83A ILE* 3.4 34.8 - - + -
105B ALA 2.9 9.6 + - - +
106B LEU 3.4 8.1 - - - +
108B LEU* 1.3 76.8 - - - +
110B THR* 1.3 67.4 + - - +
112B LEU* 3.2 8.8 + - - +
113B LEU* 2.9 20.8 + - + +
194B VAL* 4.1 22.0 - - + -
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 2.6 24.8 + - - +
107B SER* 3.8 4.9 - - - -
109B VAL* 1.3 73.7 - - - +
111B PHE* 1.3 67.2 + - - +
113B LEU* 3.1 10.1 + - - +
114B ALA* 2.9 20.6 + - - +
152B ILE* 3.9 13.2 - - + -
156B SER* 3.1 28.2 + - - +
193B VAL* 4.0 9.2 - - - +
194B VAL* 4.6 7.0 - - - +
197B VAL* 3.4 35.5 - - + +
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ALA* 4.2 22.9 - - + -
82B LEU* 3.7 26.9 - - + -
85B VAL* 4.1 9.2 - - + -
107B SER 2.9 20.5 + - - +
108B LEU 3.4 4.5 - - - +
110B THR* 1.3 75.3 - - - +
112B LEU* 1.3 66.1 + - + +
114B ALA* 2.8 15.8 + - + +
115B THR* 3.1 18.3 + - + -
140B LEU 3.7 17.5 - - - -
141B MET* 3.5 27.1 - - + -
145B GLY 4.3 0.2 - - - -
148B VAL* 3.6 30.1 - - + -
149B ALA* 3.7 14.4 - - + -
152B ILE* 3.7 24.7 - - + -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA* 4.6 5.4 - - + -
79A ILE* 3.4 45.3 - - + -
82A LEU* 3.8 12.8 - - + -
82B LEU* 4.3 11.7 - - + -
108B LEU* 3.2 15.7 + - + +
109B VAL* 3.2 8.6 + - - +
111B PHE* 1.3 79.3 - - + +
113B LEU* 1.3 58.8 + - - +
115B THR* 2.6 33.7 + - - +
117B PHE* 3.6 22.7 - - + -
136B ILE* 4.5 8.7 - - + -
141B MET* 4.1 32.8 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.5 42.2 - - + +
72A PRO* 3.6 12.8 - - + -
75A ALA* 3.6 17.5 - - + +
109B VAL* 2.9 14.2 + - + +
110B THR* 3.1 10.7 + - - +
112B LEU* 1.3 72.6 - - - +
114B ALA* 1.3 60.2 - - - +
117B PHE* 5.3 0.7 - - - -
194B VAL* 3.4 42.6 - - + +
197B VAL* 4.3 6.1 - - + -
198B TRP* 3.7 24.0 - - + +
201B ARG* 3.3 26.6 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR 2.9 10.3 + - - +
111B PHE* 2.8 20.3 + - + +
113B LEU* 1.3 75.0 - - - +
115B THR* 1.3 63.5 + - + +
116B PRO* 4.0 4.9 - - - +
148B VAL* 5.0 2.7 - - + -
152B ILE* 4.5 10.8 - - + -
197B VAL* 4.3 12.6 - - + -
201B ARG* 4.1 16.5 + - - +
212B ILE* 4.2 40.4 + - + +
213B HIS 5.4 0.2 + - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 3.1 24.1 + - + +
112B LEU* 2.6 28.1 + - - +
113B LEU 4.3 0.9 - - - +
114B ALA* 1.3 83.8 - - + +
116B PRO* 1.4 72.2 - - + +
117B PHE* 3.5 9.5 - - - -
137B PRO* 5.5 2.4 - - - +
140B LEU* 4.2 32.8 - - + +
141B MET* 4.0 14.4 - - - +
148B VAL* 5.0 6.3 - - + -
201B ARG* 4.4 2.5 + - - -
213B HIS* 4.5 17.3 - - + +
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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
------------------------------------------------------------
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