Contacts of the helix formed by residues 114 - 132 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP* 1.3 79.9 - - - +
115A LEU* 1.3 64.1 + - - +
116A LEU* 3.1 3.2 + - - +
117A SER* 3.2 17.8 + - - -
118A HIS* 3.0 22.2 + - - +
13B GLN* 4.1 26.1 + - - +
17B ASP* 5.1 2.4 + - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP* 3.6 10.0 - - - +
114A SER* 1.3 79.3 - - - +
116A LEU* 1.3 63.3 + - + +
118A HIS* 3.3 14.8 - - + +
119A VAL* 2.9 40.4 + - + +
194A SER* 6.1 1.8 - - - -
195A ASP* 4.1 31.4 - - + +
196A ILE* 5.5 17.9 - - + -
17B ASP* 5.6 0.7 - - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 5.6 12.6 - - + -
18A VAL* 4.1 26.0 - - + -
114A SER* 3.1 1.2 - - - +
115A LEU* 1.3 81.2 - - + +
117A SER* 1.3 60.4 + - - +
119A VAL* 3.8 5.4 - - + +
120A GLU* 2.9 49.8 + - + +
196A ILE* 6.2 3.4 - - + -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.2 25.1 + - - -
116A LEU* 1.3 77.9 - - - +
118A HIS* 1.3 62.6 + - - +
120A GLU* 3.5 9.4 + - - +
121A GLN* 3.1 31.0 + - - +
13B GLN* 3.4 23.1 + - - +
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER 3.0 12.4 + - - +
115A LEU* 3.3 21.3 - - + +
117A SER* 1.3 76.7 + - - +
119A VAL* 1.3 69.0 + - + +
121A GLN* 3.1 14.4 + - - +
122A LEU* 3.1 35.4 + - + +
194A SER* 5.2 6.6 - - - -
13B GLN* 3.9 8.2 - - + +
14B VAL* 3.8 29.3 - - + +
17B ASP* 2.7 40.1 + - + +
18B VAL* 5.0 6.1 - - + -
116B LEU* 4.6 8.6 - - + +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.3 14.4 - - + -
115A LEU* 2.9 25.4 + - + +
116A LEU* 3.9 5.4 - - + +
118A HIS* 1.3 81.3 - - + +
120A GLU* 1.4 56.7 + - + +
122A LEU* 3.0 7.8 + - - +
123A LEU* 2.8 45.9 + - + +
192A MET* 4.3 11.4 - - + -
194A SER* 4.3 22.0 - - - +
196A ILE* 4.2 25.1 - - + -
197A LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.3 9.1 - - + +
21A GLU* 5.3 5.9 - - - +
48A TYR* 3.7 40.4 - - + +
116A LEU* 2.9 36.7 + - + +
117A SER* 3.9 7.8 - - - +
119A VAL* 1.4 75.7 - - + +
121A GLN* 1.3 59.4 + - + +
123A LEU* 3.3 6.4 + - + +
124A ALA* 2.9 27.5 + - - +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR 6.0 0.2 - - - -
117A SER* 3.1 15.8 + - - +
118A HIS 3.1 9.4 + - - +
120A GLU* 1.3 78.4 - - + +
122A LEU* 1.3 61.1 + - - +
124A ALA* 3.4 16.2 - - - +
10B ASN* 3.3 36.6 + - - +
11B PHE* 3.1 37.8 - - + -
13B GLN* 3.0 38.5 + - - +
14B VAL* 3.3 14.2 + - + -
76B GLU* 5.3 3.2 + - - -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 3.1 36.2 + - + +
119A VAL* 3.0 8.8 + - - +
121A GLN* 1.3 76.1 - - - +
123A LEU* 1.3 65.1 + - - +
125A ALA* 3.1 22.1 + - + +
126A PHE* 3.5 10.9 - - - -
192A MET* 3.9 32.0 - - + +
193A THR 3.8 21.1 - - - +
194A SER* 4.4 2.7 - - - -
11B PHE* 4.7 8.5 - - + -
14B VAL* 4.0 13.9 - - + -
116B LEU* 3.9 22.4 - - + -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.7 30.3 - - + -
19A LEU* 5.3 1.3 - - + -
22A PHE* 3.8 33.5 - - + -
48A TYR* 4.1 17.5 - - + -
119A VAL* 2.8 22.2 + - + +
120A GLU* 3.3 7.8 + - - +
122A LEU* 1.3 76.7 - - - +
124A ALA* 1.3 62.3 + - - +
126A PHE* 3.0 20.0 + - + +
127A ILE* 3.3 13.7 + - - +
192A MET* 3.6 24.2 - - + -
197A LEU* 4.6 5.6 - - + -
199A MET* 3.7 22.2 - - + -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.7 30.4 - - + +
50A VAL* 4.2 12.1 - - + +
120A GLU 2.9 13.3 + - - +
121A GLN* 3.4 15.5 - - - +
122A LEU 3.2 0.4 - - - -
123A LEU* 1.3 74.2 - - - +
125A ALA* 1.3 57.1 + - - +
127A ILE* 3.2 9.5 + - - +
128A LEU* 2.9 36.3 + - + +
11B PHE* 5.2 3.8 - - + -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLN 3.7 2.0 + - - -
122A LEU* 3.1 14.7 + - + +
123A LEU 3.1 0.8 - - - -
124A ALA* 1.3 78.9 - - - +
126A PHE* 1.3 61.1 + - - +
128A LEU* 3.4 9.4 + - - +
129A LYS* 3.1 30.0 + - - +
190A LYS* 3.6 29.6 - - + -
11B PHE* 4.3 18.5 - - + -
110B ILE* 4.1 13.1 - - + +
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.7 17.7 - + + -
100A PHE* 5.0 0.4 - + - -
122A LEU 3.5 13.7 - - - -
123A LEU* 3.0 13.7 + - - +
125A ALA* 1.3 72.5 - - - +
127A ILE* 1.3 60.9 + - - +
129A LYS* 3.2 4.3 + - - +
130A ILE* 2.9 35.1 + - + +
190A LYS* 3.5 44.2 - - + -
192A MET* 3.7 34.8 - - + -
199A MET* 3.5 41.1 - - + -
201A LEU* 3.6 35.6 - - + +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.8 22.4 - - + -
25A VAL* 4.0 22.9 - - + -
26A ALA* 4.4 14.6 - - + -
29A LEU* 3.6 15.6 - - + +
48A TYR* 4.2 19.1 - - + -
50A VAL* 3.5 23.6 - - + -
51A PRO 4.3 3.4 - - - +
52A VAL* 3.6 19.1 - - + -
123A LEU 3.3 11.0 + - - +
124A ALA* 3.4 7.9 - - - +
126A PHE* 1.3 78.2 - - - +
128A LEU* 1.3 55.6 + - - +
130A ILE* 3.2 2.9 + - + -
131A SER* 2.9 29.5 + - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.0 32.3 - - + -
51A PRO* 5.2 6.5 - - + +
124A ALA* 2.9 24.1 + - + +
125A ALA* 3.6 6.1 - - - +
126A PHE 3.3 0.2 - - - -
127A ILE* 1.3 75.5 - - + +
129A LYS* 1.3 62.9 - - - +
131A SER* 3.1 25.6 + - - +
132A VAL* 3.4 12.8 + - - +
11B PHE* 4.9 8.1 - - + -
110B ILE* 4.0 34.1 - - + -
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA 3.1 14.6 + - - +
126A PHE* 3.6 8.1 - - - +
128A LEU* 1.3 75.2 - - - +
130A ILE* 1.3 64.9 + - - +
132A VAL* 3.4 15.6 + - + +
133A CYS* 3.3 21.3 + - - +
188A PRO 5.5 0.7 - - - -
189A LEU* 3.2 53.2 - - + +
190A LYS* 4.3 4.3 - - + -
110B ILE* 2.7 46.1 + - + +
111B SER* 4.1 0.6 - - - +
112B SER* 3.8 15.5 - - - +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 3.9 30.1 - - + -
29A LEU* 3.6 23.8 - - + -
30A ILE* 4.0 30.7 - - + +
33A VAL* 3.7 11.7 - - + +
98A PHE* 5.2 1.1 - - + -
100A PHE* 4.5 1.1 - - + -
126A PHE* 2.9 22.9 + - + +
127A ILE* 3.2 11.6 + - + +
129A LYS* 1.3 75.5 - - - +
131A SER* 1.3 63.6 + - - +
132A VAL 3.1 1.2 + - - -
133A CYS* 3.1 26.2 + - - -
189A LEU* 4.4 4.7 - - + -
201A LEU* 3.8 27.1 - - + -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.1 14.4 - - - -
33A VAL* 4.0 18.5 - - - +
51A PRO 5.2 8.1 - - - -
127A ILE* 2.9 16.5 + - - -
128A LEU* 3.1 15.4 + - - +
129A LYS 3.2 0.4 - - - -
130A ILE* 1.3 77.9 - - - +
132A VAL* 1.3 67.8 + - - +
133A CYS 3.6 0.2 - - - -
134A ASP* 3.8 9.0 - - - +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 3.6 13.7 - - - +
129A LYS* 3.6 19.7 - - + +
130A ILE 3.0 0.8 - - - -
131A SER* 1.3 91.9 + - - +
133A CYS* 1.4 53.0 - - - +
134A ASP* 3.1 11.6 - - - +
135A ALA* 3.0 30.2 + - + +
136A VAL* 5.2 0.7 - - - +
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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