Contacts of the helix formed by residues 99 - 115 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 1.3 77.1 - - - +
100C ALA* 1.3 60.7 + - - +
102C ALA* 3.5 26.2 + - + +
103C SER* 3.1 24.6 + - - -
160C TYR* 4.0 11.1 + - - +
164C VAL* 6.1 0.2 - - - +
182C ARG* 2.5 64.3 + - - +
443C ZDM 4.7 1.2 - - - +
444C CIT 4.1 19.2 + - - +
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Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.2 50.9 - - + +
93C GLY* 5.0 0.7 - - - -
94C GLU* 4.1 14.6 - - + +
98C VAL 3.1 8.1 + - - +
99C ASP* 1.3 72.4 + - - +
101C LEU* 1.3 65.8 + - - +
102C ALA 2.8 6.4 + - - -
103C SER* 3.3 6.2 + - - -
104C GLY* 2.9 20.8 + - - -
444C CIT 5.3 1.6 + - - -
90D TYR* 5.7 0.2 - - - +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.5 2.4 - - + -
90C TYR* 3.6 7.7 - - + -
99C ASP* 3.6 1.4 + - - -
100C ALA* 1.3 76.7 - - - +
102C ALA* 1.3 57.0 + - - +
105C ALA* 3.3 24.5 + - - +
182C ARG* 3.3 27.7 - - - +
443C ZDM 4.4 15.9 - - + +
31D LEU* 3.8 27.5 - - + +
86D PHE* 3.7 27.6 - - + -
87D GLY* 5.3 3.6 - - - +
90D TYR* 3.2 46.1 + - + +
91D ARG* 6.5 0.7 - - + -
94D GLU* 5.9 0.4 - - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASP* 3.5 27.3 + - + +
100C ALA 2.8 1.6 - - - -
101C LEU* 1.3 76.9 - - - +
103C SER* 1.3 55.6 + - - +
104C GLY 2.9 1.7 + - - -
105C ALA* 3.1 3.4 + - - +
106C LEU* 2.7 37.0 + - - +
160C TYR* 3.6 19.1 - - + +
186C ALA* 4.9 0.2 - - + -
443C ZDM 3.6 35.5 - - + +
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA* 3.2 25.4 + - - +
93C GLY* 3.7 7.3 - - - -
98C VAL* 4.8 0.2 - - - -
99C ASP 3.1 17.2 + - - -
100C ALA* 3.3 10.9 + - - -
102C ALA* 1.3 78.3 - - - +
104C GLY* 1.3 59.2 + - - +
106C LEU* 3.5 10.0 - - - +
107C SER* 3.4 23.2 + - - -
157C THR* 3.8 15.0 + - - -
160C TYR* 3.8 23.3 - - - -
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.3 28.1 - - - -
89C ALA* 4.1 3.8 - - - -
90C TYR* 4.1 16.2 - - - -
100C ALA 2.9 12.7 + - - -
103C SER* 1.3 76.5 + - - +
105C ALA* 1.3 64.9 + - - +
106C LEU 2.9 1.3 - - - -
107C SER* 2.9 14.4 + - - -
108C LEU 3.0 10.2 + - - -
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 3.2 15.4 - - + -
101C LEU 3.3 18.8 + - - +
102C ALA 3.1 3.7 + - - +
104C GLY* 1.3 74.4 - - - +
106C LEU* 1.3 62.0 + - - +
108C LEU* 3.8 7.0 - - - +
109C VAL* 3.2 28.2 + - - +
443C ZDM 5.5 0.2 - - + -
31D LEU* 3.9 29.2 - - + -
35D PHE* 3.9 11.2 - - + -
83D ILE* 4.8 5.5 - - + +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ALA 2.7 20.8 + - - +
103C SER* 3.5 10.1 - - - +
104C GLY 2.9 0.2 - - - -
105C ALA* 1.3 76.0 - - - +
107C SER* 1.3 58.4 + - - +
109C VAL* 3.5 1.7 + - - +
110C THR* 2.9 36.2 + - - +
156C SER* 4.7 7.4 - - - +
157C THR 5.4 0.2 - - - +
160C TYR* 4.0 33.4 - - + -
190C GLY* 4.4 14.4 - - - -
193C VAL* 3.7 31.6 - - + -
194C VAL* 4.4 15.5 - - + -
443C ZDM 5.5 4.0 - - + -
35D PHE* 3.9 23.3 - - + -
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.5 15.2 - - - +
89C ALA* 3.2 33.7 - - - +
103C SER 3.4 4.6 + - - -
104C GLY 2.9 3.7 + - - -
106C LEU* 1.3 75.1 - - - +
108C LEU* 1.3 60.8 + - - +
110C THR* 3.6 8.1 - - - -
111C PHE* 3.1 26.5 + - - +
152C ILE* 3.7 3.2 - - - +
153C ALA* 3.8 11.7 + - - -
156C SER* 3.2 25.4 - - - -
157C THR* 3.9 0.3 + - - -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 3.4 45.3 - - + +
85C VAL* 4.2 7.1 - - + +
86C PHE* 4.5 15.5 - - + -
104C GLY 3.0 9.9 + - - +
105C ALA* 3.8 12.1 - - - +
107C SER* 1.3 77.7 - - - +
109C VAL* 1.3 63.5 + - - +
110C THR 3.2 0.5 + - - -
111C PHE* 3.3 2.6 + - - +
112C LEU* 3.3 30.9 + - + +
79D ILE* 5.0 2.9 - - + -
82D LEU* 4.4 21.1 - - + +
83D ILE* 4.7 16.8 - - + +
86D PHE* 5.8 3.4 - - + -
108D LEU* 3.9 28.3 - - + -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA 3.2 16.9 + - - +
106C LEU 3.6 4.7 - - - +
108C LEU* 1.3 81.4 - - + +
110C THR* 1.3 61.5 + - - +
112C LEU* 3.9 4.7 + - - +
113C LEU* 3.3 20.3 + - + +
194C VAL* 4.8 12.1 - - + -
35D PHE* 3.5 29.2 - - + -
75D ALA* 3.6 26.6 - - + +
76D THR* 4.4 8.5 - - + -
79D ILE* 5.1 2.2 - - + -
83D ILE* 3.5 35.0 - - + -
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 2.9 32.3 + - - +
107C SER* 4.0 3.8 - - - -
108C LEU 3.1 0.4 - - - -
109C VAL* 1.3 76.7 - - - +
111C PHE* 1.3 65.9 + - - +
112C LEU 3.3 0.4 - - - -
113C LEU* 3.1 7.7 + - - +
114C ALA* 2.9 20.3 + - - +
152C ILE* 3.7 9.0 - - + -
156C SER* 3.3 25.7 + - - +
193C VAL* 4.3 2.8 - - - +
194C VAL* 4.5 9.2 - - - +
197C VAL* 3.2 38.3 - - + +
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.7 38.4 - - + -
82C LEU* 4.1 16.6 - - + -
85C VAL* 3.6 23.3 - - + -
107C SER 3.1 19.9 + - - +
108C LEU 3.6 4.9 - - - +
110C THR* 1.3 75.8 - - - +
112C LEU* 1.3 55.9 + - + +
114C ALA* 2.7 27.7 + - + +
115C THR* 3.0 20.1 + - + -
140C LEU 4.0 15.3 - - - -
141C MET* 4.1 12.8 - - + -
145C GLY 3.8 2.0 - - - -
148C VAL* 3.1 35.2 - - + -
149C ALA* 3.7 10.1 - - - -
152C ILE* 3.4 16.0 - - + +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.7 13.7 - - + -
108C LEU* 3.3 19.9 + - + +
109C VAL* 4.1 4.9 - - - +
110C THR 3.3 0.4 - - - -
111C PHE* 1.3 76.0 - - + +
113C LEU* 1.3 58.9 + - - +
115C THR* 2.7 27.3 - - - +
117C PHE* 3.2 26.0 - - + -
136C ILE* 4.6 12.3 - - + -
141C MET* 3.7 34.1 - - + -
201C ARG* 4.7 0.5 + - - -
75D ALA* 4.4 4.3 - - + -
79D ILE* 3.6 41.7 - - + -
82D LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 3.3 14.4 + - + +
110C THR* 3.1 11.2 + - - +
112C LEU* 1.3 78.4 - - - +
114C ALA* 1.3 56.8 + - - +
117C PHE* 5.2 0.4 - - - -
194C VAL* 3.7 21.5 - - + +
197C VAL* 4.2 10.8 - - + -
198C TRP* 3.6 37.7 - - + +
201C ARG* 3.1 29.6 + - - +
71D TYR* 3.4 14.1 - - + +
72D PRO* 3.3 45.8 - - + -
75D ALA* 3.6 9.3 - - + +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR 2.9 11.1 + - - +
111C PHE* 2.7 17.1 + - + +
113C LEU* 1.3 77.9 - - - +
115C THR* 1.3 66.2 + - + +
116C PRO* 4.1 4.5 - - - +
148C VAL* 6.3 1.3 - - + -
152C ILE* 4.5 17.3 - - + -
197C VAL* 4.6 5.8 - - + -
201C ARG* 4.2 11.8 - - - +
211C SER* 5.4 0.7 - - - -
212C ILE* 4.1 41.6 + - + +
213C HIS 5.0 0.3 + - - -
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Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C PHE* 3.0 18.7 + - + +
112C LEU* 2.7 23.8 + - - +
114C ALA* 1.3 85.4 - - + +
116C PRO* 1.3 69.4 - - - +
117C PHE* 3.7 6.6 - - - -
136C ILE* 5.8 2.4 - - - +
137C PRO* 5.2 2.9 - - - +
140C LEU* 4.0 23.3 - - + +
141C MET* 3.7 19.8 - - + +
148C VAL* 4.8 13.7 - - + -
201C ARG* 4.4 1.3 - - - -
212C ILE* 6.3 0.4 - - + -
213C HIS* 4.1 26.5 - - + +
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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