Contacts of the helix formed by residues 108 - 123 (chain C) in PDB entry 2Q2U
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 LYS 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B THR* 3.2 32.8 + - - +
198B ILE* 6.1 1.1 - - - -
239B ASP* 3.6 26.5 + - - +
241B ASP* 5.1 7.3 - - - +
270B MET* 6.1 0.6 - - - +
106C LEU 3.5 3.6 + - - +
107C LYS* 1.3 74.7 - - - +
109C TYR* 1.3 68.0 + - - +
110C ILE* 3.9 11.7 - - + -
111C ASP* 2.8 33.9 + - - +
112C ARG 2.9 10.4 + - - -
168C PRO 3.9 2.5 - - - +
169C ASP* 3.4 45.5 - - + +
170C GLY 3.4 0.2 - - - -
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Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.6 22.2 - - + -
25C THR* 3.9 11.7 - - + +
98C PHE* 3.8 18.3 + - - +
99C ASP* 4.6 3.8 - - - -
108C LYS* 1.3 68.9 - - - +
110C ILE* 1.3 63.7 + - - +
112C ARG* 2.9 20.5 + - + +
113C VAL* 2.8 38.6 + - + +
137C LEU 4.0 2.3 + - - -
139C PRO* 3.5 44.3 - - + +
166C ARG* 3.2 60.4 + - + -
167C LYS 3.8 9.6 - - - +
168C PRO 3.2 10.9 + - - +
170C GLY* 2.8 14.5 + - - +
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Residues in contact with ILE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.4 28.3 - - + -
108C LYS* 3.9 18.2 - - + -
109C TYR* 1.3 75.5 - - - +
111C ASP* 1.3 63.3 + - - +
113C VAL* 3.2 11.0 + - + +
114C GLU* 2.9 27.1 + - - +
139C PRO* 5.7 0.9 - - + -
168C PRO* 3.1 30.7 + - + +
169C ASP* 4.6 1.3 - - + +
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Residues in contact with ASP 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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239B ASP* 4.0 5.9 - - - +
241B ASP* 4.9 4.9 - - - +
242B GLY* 4.2 21.2 + - - -
107C LYS* 3.4 19.5 - - + -
108C LYS* 2.8 44.4 + - - +
110C ILE* 1.3 75.4 - - - +
112C ARG* 1.3 59.4 + - - +
114C GLU* 3.0 10.5 + - - +
115C ASP* 2.8 35.3 + - - +
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Residues in contact with ARG 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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7C LEU* 4.4 1.0 - - - +
99C ASP* 2.8 43.9 + - - +
100C TYR* 3.6 29.2 - - - +
101C VAL* 4.8 4.9 - - - +
104C ASP 5.2 3.8 - - - -
105C PRO* 5.0 1.1 + - - -
107C LYS* 2.8 59.2 + - + +
108C LYS 2.9 7.7 + - - +
109C TYR* 2.9 17.0 + - + +
111C ASP* 1.3 76.4 - - - +
113C VAL* 1.3 62.6 + - + +
115C ASP* 3.3 10.5 + - - +
116C MET* 3.1 19.2 + - - +
166C ARG* 3.5 13.1 - - - +
170C GLY 3.1 18.4 + - - -
171C LYS 3.4 13.7 + - - -
172C TYR* 3.5 29.1 - - - +
183C ILE* 5.8 0.2 - - - +
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Residues in contact with VAL 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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98C PHE 5.3 3.1 - - - +
99C ASP* 6.4 1.6 - - - +
109C TYR* 2.8 55.9 + - + +
110C ILE* 3.3 8.3 - - + +
112C ARG* 1.3 75.6 - - - +
114C GLU* 1.3 54.1 + - - +
116C MET* 2.7 33.9 + - + +
117C LYS* 2.7 29.4 + - + +
137C LEU 5.2 0.4 - - - +
138C ILE* 4.0 22.4 - - + -
139C PRO* 3.7 24.7 - - + -
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Residues in contact with GLU 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 ILE 2.9 13.6 + - - +
111C ASP* 3.0 16.8 + - - +
113C VAL* 1.3 76.4 - - - +
115C ASP* 1.3 58.1 + - - +
117C LYS* 3.1 28.1 + - - +
118C ASN* 2.8 53.5 + - - +
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Residues in contact with ASP 115 (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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100C TYR* 3.8 17.9 - - + +
102C THR* 3.4 20.7 + - + +
107C LYS* 3.1 33.6 + - - +
111C ASP* 2.8 23.3 + - - +
112C ARG* 3.4 11.7 - - - +
114C GLU* 1.3 77.2 - - - +
116C MET* 1.3 62.4 + - - +
118C ASN* 3.7 8.8 - - - +
119C TYR* 3.1 22.9 + - - +
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Residues in contact with MET 116 (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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97C TRP* 3.2 72.9 - - + +
98C PHE* 4.2 2.5 - - - -
99C ASP* 4.1 13.0 - - - +
100C TYR* 3.8 11.9 - - + -
112C ARG 3.1 11.8 + - - +
113C VAL* 2.7 20.2 + - + +
115C ASP* 1.3 75.8 - - - +
117C LYS* 1.3 63.0 + - - +
119C TYR* 3.4 4.7 + - - +
120C ILE* 3.2 26.1 + - + +
136C PRO* 3.6 23.8 - - + -
137C LEU 3.8 7.2 - - - +
138C ILE* 3.7 18.2 - - + -
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Residues in contact with LYS 117 (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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113C VAL* 2.7 37.6 + - + +
114C GLU* 3.5 32.4 + - - +
116C MET* 1.3 72.8 - - - +
118C ASN* 1.3 66.5 + - - +
120C ILE* 3.1 21.9 + - - +
121C THR* 3.1 17.3 + - - -
138C ILE* 4.3 26.6 - - + +
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Residues in contact with ASN 118 (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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114C GLU* 2.8 41.3 + - - +
115C ASP* 3.7 8.7 - - - +
117C LYS* 1.3 78.2 - - - +
119C TYR* 1.3 66.0 + - - +
121C THR* 2.9 22.1 + - - -
122C VAL* 3.1 19.8 + - + +
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Residues in contact with TYR 119 (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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59C LEU 4.0 13.4 + - - -
61C PRO* 3.3 40.1 - - + +
97C TRP* 3.8 21.8 - + + -
100C TYR* 3.9 16.2 - + + -
115C ASP 3.1 12.1 + - - +
116C MET 3.6 9.2 - - - +
117C LYS 3.4 0.2 - - - -
118C ASN* 1.3 78.7 - - - +
120C ILE* 1.3 56.9 + - - +
122C VAL* 3.3 5.1 + - - -
123C HIS* 2.9 77.7 + + + +
126C ILE* 4.4 9.6 - - + +
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Residues in contact with ILE 120 (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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97C TRP* 4.1 15.0 - - + -
116C MET* 3.2 19.1 - - + +
117C LYS* 3.2 14.8 - - - +
118C ASN 3.0 0.4 - - - -
119C TYR* 1.3 72.5 - - - +
121C THR* 1.3 69.0 + - - +
122C VAL 3.0 1.6 - - - -
123C HIS 2.9 11.0 + - - +
124C PRO* 2.9 21.5 - - + +
126C ILE* 4.1 12.6 - - + -
127C LEU* 3.4 27.4 - - + -
136C PRO* 3.5 36.1 - - + -
138C ILE* 5.3 2.5 - - + -
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Residues in contact with THR 121 (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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117C LYS 3.1 13.3 + - - -
118C ASN* 2.9 14.8 + - - -
120C ILE* 1.3 78.8 - - - +
122C VAL* 1.3 59.6 + - + +
124C PRO* 3.2 20.8 - - - +
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Residues in contact with VAL 122 (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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118C ASN* 3.1 18.3 + - + +
119C TYR* 3.6 3.4 - - - +
120C ILE 3.0 0.6 - - - -
121C THR* 1.3 81.9 - - - +
123C HIS* 1.3 86.4 + - + +
124C PRO* 3.3 5.8 - - - +
125C HIS* 4.4 2.9 - - - -
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Residues in contact with HIS 123 (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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119C TYR* 2.9 63.1 + + + +
120C ILE 2.9 6.7 + - - -
122C VAL* 1.3 104.4 - - + +
124C PRO* 1.3 64.9 - - - +
125C HIS* 3.0 33.4 + + + +
126C ILE* 3.0 31.8 + - + +
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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