Contacts of the helix formed by residues 108 - 123 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D LEU 3.5 4.8 + - - +
107D LYS* 1.3 74.3 - - - +
109D TYR* 1.3 67.3 + - - +
110D ILE* 3.9 11.2 - - + -
111D ASP* 2.8 33.1 + - - +
112D ARG 2.9 10.4 + - - -
168D PRO 3.8 2.9 - - - +
169D ASP* 3.3 45.3 - - + +
170D GLY 3.4 0.2 - - - -
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Residues in contact with TYR 109 (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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23D LEU* 3.6 22.2 - - + -
25D THR* 3.9 11.9 - - + +
98D PHE* 3.8 18.1 + - - +
99D ASP* 4.6 3.8 - - - -
108D LYS* 1.3 69.8 - - - +
110D ILE* 1.3 63.4 + - - +
112D ARG* 2.9 20.3 + - + +
113D VAL* 2.8 39.2 + - + +
137D LEU 4.0 2.3 + - - -
139D PRO* 3.5 44.3 - - + +
166D ARG* 3.2 60.7 + - + -
167D LYS 3.8 9.9 - - - +
168D PRO 3.2 10.9 + - - +
170D GLY* 2.8 14.7 + - - +
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.4 27.6 - - + -
108D LYS* 3.9 17.5 - - + -
109D TYR* 1.3 74.7 - - - +
111D ASP* 1.3 64.0 + - - +
113D VAL* 3.2 11.8 + - + +
114D GLU* 2.9 27.1 + - - +
139D PRO* 5.7 0.9 - - + -
168D PRO* 3.1 30.7 + - + +
169D ASP* 4.6 1.3 - - + +
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Residues in contact with ASP 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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107D LYS* 3.4 22.3 - - + +
108D LYS* 2.8 43.9 + - - +
110D ILE* 1.3 75.5 - - - +
112D ARG* 1.3 60.1 + - - +
114D GLU* 3.0 10.5 + - - +
115D ASP* 2.8 34.9 + - - +
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Residues in contact with ARG 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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7D LEU* 4.4 1.6 - - - +
99D ASP* 2.8 43.2 + - - +
100D TYR* 3.6 29.8 - - - +
101D VAL* 4.8 4.9 - - - +
104D ASP 5.1 4.0 - - - -
105D PRO* 5.0 0.9 + - - -
107D LYS* 2.8 59.2 + - + +
108D LYS 2.9 7.7 + - - +
109D TYR* 2.9 17.1 + - + +
111D ASP* 1.3 75.7 - - - +
113D VAL* 1.3 61.3 + - - +
115D ASP* 3.4 10.0 + - - +
116D MET* 3.1 19.8 + - - +
166D ARG* 3.5 12.5 - - - +
170D GLY 3.2 18.8 + - - -
171D LYS 3.4 13.1 + - - -
172D TYR* 3.5 31.1 - - - +
183D ILE* 5.8 0.4 - - - +
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Residues in contact with VAL 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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98D PHE 5.3 3.1 - - - +
99D ASP* 6.4 1.3 - - - +
109D TYR* 2.8 56.4 + - + +
110D ILE* 3.3 9.4 - - + +
112D ARG* 1.3 75.3 - - + +
114D GLU* 1.3 53.0 + - - +
116D MET* 2.8 18.1 + - + +
117D LYS* 2.7 44.7 + - + +
137D LEU 5.2 0.4 - - - +
138D ILE* 4.0 22.2 - - + -
139D PRO* 3.7 23.3 - - + -
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Residues in contact with GLU 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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92C LYS* 5.8 3.5 - - - -
110D ILE 2.9 14.3 + - - +
111D ASP* 3.0 16.4 + - - +
113D VAL* 1.3 76.5 - - - +
115D ASP* 1.3 58.9 + - - +
117D LYS* 3.1 27.2 + - - +
118D ASN* 2.9 53.0 + - - +
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Residues in contact with ASP 115 (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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100D TYR* 3.7 17.3 - - + +
102D THR* 3.4 21.6 + - + +
107D LYS* 3.0 33.8 + - - +
111D ASP* 2.8 25.1 + - - +
112D ARG* 3.5 12.3 - - - +
114D GLU* 1.3 77.6 - - - +
116D MET* 1.3 61.5 + - - +
118D ASN* 3.8 8.3 - - - +
119D TYR* 3.1 22.7 + - - +
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Residues in contact with MET 116 (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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97D TRP* 3.2 74.2 - - + +
98D PHE* 4.2 2.7 - - - +
99D ASP* 4.1 13.0 - - - +
100D TYR* 3.7 12.5 - - + -
112D ARG 3.1 11.8 + - - +
113D VAL* 2.8 19.7 + - + +
115D ASP* 1.3 76.2 - - - +
117D LYS* 1.3 62.3 + - - +
119D TYR* 3.4 4.5 + - - +
120D ILE* 3.2 26.3 + - + +
136D PRO* 3.7 23.6 - - + -
137D LEU 3.8 7.2 - - - +
138D ILE* 3.7 17.9 - - + -
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Residues in contact with LYS 117 (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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113D VAL* 2.7 37.6 + - + +
114D GLU* 3.5 31.8 + - - +
116D MET* 1.3 72.2 - - - +
118D ASN* 1.3 67.5 + - - +
120D ILE* 3.1 22.9 + - - +
121D THR* 3.1 15.8 + - - -
138D ILE* 4.3 27.2 - - + +
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Residues in contact with ASN 118 (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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114D GLU* 2.9 42.0 + - - +
115D ASP* 3.8 9.1 - - - +
117D LYS* 1.3 77.4 - - - +
119D TYR* 1.3 67.1 + - - +
121D THR* 2.9 20.7 + - - -
122D VAL* 3.1 19.4 + - + +
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Residues in contact with TYR 119 (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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59D LEU 4.0 13.3 + - - -
61D PRO* 3.3 40.2 - - + +
97D TRP* 3.8 22.2 - + + -
100D TYR* 3.9 17.0 - + + -
115D ASP 3.1 12.1 + - - +
116D MET 3.6 9.0 - - - +
117D LYS 3.4 0.2 - - - -
118D ASN* 1.3 78.5 - - - +
120D ILE* 1.3 56.3 + - - +
122D VAL* 3.3 4.9 + - - -
123D HIS* 2.9 77.5 + + + +
126D ILE* 4.4 9.6 - - + +
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D TRP* 4.1 15.7 - - + -
116D MET* 3.2 19.5 - - + +
117D LYS* 3.2 14.8 - - - +
118D ASN 3.0 0.4 - - - -
119D TYR* 1.3 73.1 - - - +
121D THR* 1.3 67.9 + - - +
122D VAL 3.0 1.6 - - - -
123D HIS 2.8 11.0 + - - +
124D PRO* 2.9 21.6 - - + +
126D ILE* 4.1 12.6 - - + -
127D LEU* 3.4 27.6 - - + -
136D PRO* 3.5 35.7 - - + -
138D ILE* 5.3 2.5 - - + -
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Residues in contact with THR 121 (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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117D LYS 3.1 12.8 + - - -
118D ASN* 2.9 15.6 + - - -
120D ILE* 1.3 78.8 - - - +
122D VAL* 1.3 60.5 + - + +
124D PRO* 3.2 20.1 - - - +
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Residues in contact with VAL 122 (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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118D ASN* 3.1 18.6 + - + +
119D TYR* 3.6 2.7 - - - +
120D ILE 3.0 0.6 - - - -
121D THR* 1.3 82.1 - - + +
123D HIS* 1.3 87.7 + - + +
124D PRO* 3.3 5.6 - - - +
125D HIS* 4.4 2.9 - - - -
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Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D TYR* 2.9 61.8 + + + +
120D ILE 2.8 6.9 + - - -
122D VAL* 1.3 104.6 - - + +
124D PRO* 1.3 64.1 - - - +
125D HIS* 3.0 33.5 + + + +
126D 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