Contacts of the helix formed by residues 113 - 125 (chain B) in PDB entry 2Q8D
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 GLU 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A VAL* 5.6 5.7 - - - +
341A ILE 5.4 3.1 - - - +
111B TYR* 3.3 16.2 - - - -
112B SER* 1.3 84.2 + - - +
114B PHE* 1.3 64.4 + - - +
115B GLU* 4.0 22.0 - - - +
116B GLU* 3.2 31.8 + - + +
117B LEU 3.5 0.2 + - - -
119B ARG* 5.1 7.1 + - - -
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Residues in contact with PHE 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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111B TYR* 4.4 6.6 - - + -
113B GLU* 1.3 71.4 - - - +
115B GLU* 1.3 73.7 + - - +
117B LEU* 3.0 9.5 + - + +
118B GLU* 2.7 71.3 + - + +
207B SER* 3.0 34.8 - - - -
209B TYR* 4.6 3.4 - + - -
259B LYS* 4.0 20.2 - - + -
260B VAL 6.3 0.9 - - - -
261B THR* 3.9 11.0 - - - +
279B PHE* 3.8 15.7 - + - -
281B HIS* 3.9 15.7 - + - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLU* 3.4 21.1 - - - +
114B PHE* 1.3 98.4 + - - +
116B GLU* 1.3 57.6 + - - +
118B GLU* 3.5 14.5 - - - +
119B ARG* 2.9 51.0 + - - +
259B LYS* 5.4 4.2 + - - +
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Residues in contact with GLU 116 (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 ARG* 4.5 1.7 - - - +
111B TYR* 3.4 11.3 - - + -
112B SER* 2.9 32.7 + - - -
113B GLU* 3.2 19.5 + - + +
114B PHE 3.1 0.8 - - - -
115B GLU* 1.3 77.7 - - - +
117B LEU* 1.3 58.6 + - - +
119B ARG* 3.2 28.3 + - - +
120B LYS* 3.0 56.0 + - + +
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Residues in contact with LEU 117 (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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108B THR* 3.8 11.9 - - + -
109B PRO* 3.9 13.2 - - + -
111B TYR* 3.7 47.9 - - + +
113B GLU 3.5 1.6 + - - -
114B PHE* 3.0 9.5 + - + +
116B GLU* 1.3 79.3 - - - +
118B GLU* 1.3 56.3 + - - +
120B LYS* 3.4 4.3 + - + +
121B TYR* 2.9 27.7 + - - +
181B TRP* 3.7 33.0 - - + -
279B PHE* 4.5 3.5 - - + -
281B HIS* 3.6 43.7 - - + +
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Residues in contact with GLU 118 (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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114B PHE* 2.7 45.1 + - + +
115B GLU* 3.5 16.4 - - - +
117B LEU* 1.3 70.3 - - - +
119B ARG* 1.3 66.3 + - + +
121B TYR* 3.3 1.6 + - - +
122B TRP* 3.1 37.3 + - + -
209B TYR* 2.4 34.2 + - - +
247B PRO* 3.8 5.4 - - - +
259B LYS* 2.8 33.9 + - - +
279B PHE* 4.1 10.9 - - + -
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Residues in contact with ARG 119 (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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113B GLU* 5.1 7.9 + - - -
115B GLU* 2.9 43.9 + - + +
116B GLU* 3.2 33.4 + - - +
118B GLU* 1.3 78.4 - - + +
120B LYS* 1.3 56.9 + - + +
122B TRP* 3.4 4.4 + - - +
123B LYS* 3.0 32.7 + - - +
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Residues in contact with LYS 120 (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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109B PRO* 3.8 26.9 - - + -
110B ARG* 3.2 36.8 + - - +
116B GLU* 3.0 43.9 + - + +
117B LEU* 3.7 10.1 - - + +
118B GLU 3.3 0.4 - - - -
119B ARG* 1.3 72.6 - - + +
121B TYR* 1.3 64.9 + - - +
123B LYS* 4.5 5.6 - - + -
124B ASN* 2.8 44.9 + - - +
181B TRP* 4.3 12.5 - - + -
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Residues in contact with TYR 121 (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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117B LEU 2.9 15.1 + - - +
118B GLU 3.4 7.2 - - - +
119B ARG 3.2 0.2 - - - -
120B LYS* 1.3 77.6 - - - +
122B TRP* 1.3 103.2 + + - +
124B ASN 3.8 0.2 - - - -
125B LEU* 3.0 58.4 + - + +
181B TRP* 3.8 11.4 - + + -
182B LYS* 3.7 28.0 - - + -
184B SER* 2.9 26.4 + - - -
209B TYR* 5.5 0.2 - + - -
244B LEU* 4.3 6.1 - - - +
278B GLY 4.3 1.7 + - - -
279B PHE* 3.5 48.5 - + + -
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Residues in contact with TRP 122 (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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82B PHE* 3.9 27.2 - + - -
118B GLU* 3.1 30.7 + - + +
119B ARG* 4.2 4.3 - - - +
121B TYR* 1.3 99.2 - + - +
123B LYS* 1.3 60.5 + - - +
125B LEU* 3.4 40.1 - - + +
209B TYR* 3.0 38.6 + + - -
244B LEU* 4.4 7.6 - - + -
245B ILE 3.6 16.4 - - - -
246B SER* 3.5 35.4 - - - -
247B PRO* 3.4 25.2 - - + +
248B LEU* 6.4 2.0 - - + -
277B ALA* 6.5 1.3 - - + -
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Residues in contact with LYS 123 (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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119B ARG 3.0 19.0 + - - +
120B LYS* 5.0 5.4 - - + -
122B TRP* 1.3 79.5 - - - +
124B ASN* 1.3 80.8 + - - +
125B LEU 3.6 0.8 + - - -
126B THR* 5.2 1.2 + - - -
127B PHE* 3.4 19.1 - - + -
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Residues in contact with ASN 124 (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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109B PRO* 6.3 0.2 - - - +
120B LYS* 2.8 39.6 + - - +
121B TYR 3.8 0.4 - - - -
123B LYS* 1.3 97.3 + - - +
125B LEU* 1.3 59.1 + - - +
126B THR 3.1 3.4 - - - -
127B PHE* 2.9 45.7 + - + +
181B TRP* 5.6 1.9 - - + +
182B LYS* 3.1 23.9 + - + -
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Residues in contact with LEU 125 (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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73B GLN 5.1 1.9 - - - +
75B VAL* 3.6 27.4 + - + +
82B PHE* 3.7 18.2 - - + -
84B GLN* 5.3 0.2 - - - +
121B TYR* 3.0 47.1 + - + +
122B TRP* 3.4 46.2 - - + +
123B LYS 3.6 1.2 - - - -
124B ASN* 1.3 76.0 - - - +
126B THR* 1.3 64.0 + - + +
127B PHE 4.3 0.3 - - - +
129B PRO* 5.8 0.7 - - - +
130B PRO* 5.6 1.2 - - - +
182B LYS* 3.5 19.8 + - + +
184B SER* 4.3 4.0 - - - +
244B LEU* 3.8 18.8 - - + -
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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