Contacts of the helix formed by residues 114 - 132 (chain B) in PDB entry 3ABD
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 SER 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A THR* 3.4 40.5 + - - -
192A MET* 4.4 0.6 - - - -
193A THR* 4.2 14.7 + - - -
112B SER 3.9 0.4 + - - -
113B ASP* 1.3 73.2 - - - +
115B LEU* 1.3 63.5 + - - +
116B LEU* 3.9 8.8 + - - +
117B SER* 3.2 26.6 + - - -
118B HIS* 3.0 19.1 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS* 4.0 10.0 - - - +
107B LEU* 5.5 0.9 - - + -
111B SER* 5.4 8.3 - - - +
113B ASP* 3.1 10.0 + - - +
114B SER* 1.3 69.7 - - - +
116B LEU* 1.3 51.0 + - + +
118B HIS* 2.8 34.3 + - + +
119B VAL* 2.6 51.2 + - + +
194B SER* 4.1 9.4 - - - -
195B ASP* 3.5 35.7 - - + +
196B ILE* 3.7 31.2 - - + -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 4.6 8.5 - - + +
122A LEU* 3.9 20.9 - - + -
193A THR* 3.2 34.3 - - + +
194A SER* 5.2 1.8 - - - -
14B VAL* 3.7 30.3 - - + -
18B VAL* 4.5 17.3 - - + -
114B SER* 3.9 7.9 - - - +
115B LEU* 1.3 77.0 - - - +
117B SER* 1.3 57.1 + - - +
119B VAL* 3.8 7.4 - - - +
120B GLU* 2.9 49.0 + - - +
196B ILE* 5.8 4.0 - - + +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 5.5 4.7 - - - -
114B SER* 3.1 24.5 + - - -
116B LEU* 1.3 78.7 - - - +
118B HIS* 1.3 61.5 + - - +
120B GLU* 3.4 7.7 + - - +
121B GLN* 2.8 48.4 + - - +
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASP* 5.9 4.5 - - + +
114B SER 3.0 9.0 + - - +
115B LEU* 2.8 38.1 + - + +
117B SER* 1.3 75.9 + - - +
119B VAL* 1.3 58.7 + - - -
121B GLN* 3.1 19.1 + - - +
122B LEU* 3.2 44.5 + - + +
193B THR 4.5 4.6 + - - -
194B SER* 4.2 7.5 - - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.0 17.9 - - + -
115B LEU* 2.6 44.5 + - + +
116B LEU* 3.8 7.4 - - - +
118B HIS* 1.3 73.0 - - - +
120B GLU* 1.4 59.2 + - + +
122B LEU* 3.0 11.7 + - - +
123B LEU* 2.9 46.9 + - + +
192B MET* 4.6 10.5 - - + -
194B SER* 4.0 16.4 - - - +
196B ILE* 4.2 15.3 - - + -
197B LEU* 4.9 5.4 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 5.4 9.4 - - + +
21B GLU* 4.9 8.8 - - - +
48B TYR* 3.9 37.1 - - + +
116B LEU* 2.9 35.2 + - + +
117B SER* 4.0 7.2 - - - +
119B VAL* 1.4 76.3 - - + +
121B GLN* 1.3 67.6 + - + +
123B LEU* 3.2 7.7 + - + +
124B ALA* 3.0 23.2 + - - +
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Residues in contact with GLN 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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48B TYR 5.9 0.2 - - - -
117B SER* 2.8 34.6 + - - +
118B HIS* 3.1 8.8 + - - +
120B GLU* 1.3 78.8 - - + +
122B LEU* 1.3 64.8 + - + +
124B ALA* 3.4 18.3 + - - +
125B ALA* 3.7 5.0 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B HIS* 3.2 45.5 + - + +
119B VAL* 3.0 10.4 + - - +
121B GLN* 1.3 79.8 - - + +
123B LEU* 1.3 62.0 - - - +
125B ALA* 3.1 23.2 + - + +
126B PHE* 3.4 12.8 - - - -
190B LYS* 6.4 1.6 - - - -
192B MET* 4.2 32.9 - - + +
193B THR 3.7 19.3 - - - +
194B SER* 4.5 2.2 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.0 17.7 - - + -
19B LEU* 5.2 1.1 - - + -
22B PHE* 3.7 29.7 - - + -
48B TYR* 4.1 22.0 - - + +
119B VAL* 2.9 36.0 + - + +
120B GLU* 3.2 6.0 + - + +
122B LEU* 1.3 73.0 - - - +
124B ALA* 1.3 66.5 + - - +
125B ALA 3.0 2.2 - - - -
126B PHE* 3.0 18.1 + - + +
127B ILE* 3.2 15.8 + - - +
192B MET* 3.7 13.9 - - + -
197B LEU* 4.9 3.8 - - + -
199B MET* 3.5 32.1 - - + -
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Residues in contact with ALA 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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48B TYR* 3.5 33.8 - - + +
50B VAL* 4.1 12.1 - - + +
120B GLU 3.0 10.6 + - - +
121B GLN* 3.4 15.3 - - - +
122B LEU 3.2 0.2 - - - -
123B LEU* 1.3 78.4 - - - +
125B ALA* 1.3 56.6 + - - +
127B ILE* 3.3 7.4 + - - +
128B LEU* 2.9 33.8 + - + +
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Residues in contact with ALA 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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121B GLN 3.7 4.1 + - - +
122B LEU* 3.1 16.3 + - + +
123B LEU 3.0 0.8 - - - -
124B ALA* 1.3 81.1 - - - +
126B PHE* 1.3 61.3 + - - +
128B LEU* 3.4 13.3 + - + +
129B LYS* 3.0 26.9 + - - +
190B LYS* 3.5 31.4 - - + +
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Residues in contact with PHE 126 (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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22B PHE* 3.7 17.9 - + + -
100B PHE* 5.0 0.7 - + - -
122B LEU 3.4 13.7 - - - -
123B LEU* 3.0 13.9 + - - +
125B ALA* 1.3 79.4 - - - +
127B ILE* 1.3 56.5 + - - +
129B LYS* 3.2 4.3 + - - +
130B ILE* 3.0 33.6 + - + +
190B LYS* 3.5 40.8 - - + -
191B THR 4.0 0.7 - - - -
192B MET* 3.4 46.4 - - + -
199B MET* 3.5 32.1 - - + -
201B LEU* 3.5 36.5 - - + +
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Residues in contact with ILE 127 (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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22B PHE* 3.7 23.8 - - + -
25B VAL* 4.0 21.1 - - + -
26B ALA* 4.3 16.2 - - + -
29B LEU* 3.7 12.7 - - + +
48B TYR* 4.2 17.5 - - + -
50B VAL* 3.7 14.8 - - + -
51B PRO 4.4 1.3 - - - +
52B VAL* 3.5 28.3 - - + -
123B LEU 3.2 11.6 + - - +
124B ALA* 3.5 7.9 - - - +
126B PHE* 1.3 74.0 - - - +
128B LEU* 1.4 59.0 + - - +
130B ILE* 3.3 7.2 + - + +
131B SER* 2.9 36.4 + - - +
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Residues in contact with LEU 128 (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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50B VAL* 4.0 31.2 - - + -
51B PRO* 5.2 6.5 - - + +
124B ALA* 2.9 21.3 + - + +
125B ALA* 3.6 15.0 - - + +
127B ILE* 1.4 75.2 - - + +
129B LYS* 1.3 63.7 + - + +
131B SER* 3.4 16.1 + - - +
132B VAL* 3.4 18.1 + - - +
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Residues in contact with LYS 129 (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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125B ALA 3.0 16.7 + - - +
126B PHE* 3.5 9.6 - - - +
128B LEU* 1.3 75.2 - - + +
130B ILE* 1.3 64.4 + - - +
132B VAL* 3.4 14.1 + - + +
133B CYS* 3.3 21.3 + - - +
189B LEU* 2.6 57.5 + - + +
190B LYS* 3.7 25.1 - - + +
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Residues in contact with ILE 130 (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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26B ALA* 3.9 30.7 - - + -
29B LEU* 3.7 22.2 - - + -
30B ILE* 3.9 29.6 - - + -
33B VAL* 3.6 15.1 - - + +
98B PHE* 5.1 2.7 - - + -
100B PHE* 4.6 1.3 - - + -
126B PHE* 3.0 23.8 + - + +
127B ILE* 3.7 10.8 - - + +
129B LYS* 1.3 70.3 - - - +
131B SER* 1.3 67.2 + - - +
132B VAL 3.0 3.5 + - - -
133B CYS* 3.0 26.8 + - - -
189B LEU* 4.6 4.7 - - + +
201B LEU* 3.8 26.0 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.3 20.3 - - - +
33B VAL* 4.0 13.7 - - - +
51B PRO 4.1 13.0 + - - -
127B ILE* 2.9 20.2 + - - +
128B LEU* 3.6 13.3 - - - +
129B LYS 3.3 0.4 - - - -
130B ILE* 1.3 75.9 - - - +
132B VAL* 1.3 66.1 + - - +
134B ASP* 3.5 10.7 - - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU 3.4 17.7 - - - +
129B LYS* 3.6 14.1 - - + +
131B SER* 1.3 88.7 - - - +
133B CYS* 1.3 58.6 + - - +
134B ASP* 3.1 11.1 + - - -
135B ALA* 3.3 20.3 + - + +
136B VAL* 4.7 1.4 + - - +
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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