Contacts of the helix formed by residues 114 - 134 (chain A) in PDB entry 3UX9
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 ALA 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASN* 1.3 81.2 + - - +
115A ASP* 1.3 61.2 + - - +
116A SER 3.4 0.2 - - - -
117A ILE* 4.0 11.5 - - - +
118A LEU* 3.3 23.9 + - - +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 4.9 2.3 - - - +
113A ASN* 2.3 38.9 + - - -
114A ALA* 1.3 80.2 - - - +
116A SER* 1.3 65.0 + - - +
118A LEU* 3.4 9.5 + - - +
119A ALA* 3.3 19.1 + - - +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.2 38.4 + - - -
56A VAL* 4.5 17.8 - - - +
113A ASN* 3.3 17.0 + - - +
115A ASP* 1.3 76.6 - - - +
117A ILE* 1.3 66.6 + - - +
118A LEU 2.9 3.6 + - - -
119A ALA* 3.0 13.2 + - - +
120A VAL* 3.2 17.7 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.8 37.9 - - - +
56A VAL* 4.3 14.6 - - + -
59A GLU* 3.6 28.7 - - + +
113A ASN* 3.5 22.1 + - - +
114A ALA* 4.4 7.0 - - - +
115A ASP 3.4 0.4 - - - -
116A SER* 1.3 76.7 - - - +
118A LEU* 1.3 59.0 + - - +
120A VAL* 3.6 8.8 + - - +
121A LYS* 3.1 34.5 + - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 3.3 20.5 + - - +
115A ASP* 3.5 9.0 - - - +
116A SER 2.9 0.2 - - - -
117A ILE* 1.3 78.0 - - - +
119A ALA* 1.3 60.2 + - - +
120A VAL 3.1 0.2 - - - -
121A LYS* 3.1 7.6 + - + +
122A LYS* 2.8 61.1 + - + +
125A ARG* 4.4 15.0 - - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 3.6 28.0 - - + +
42A GLU* 4.1 12.6 - - - +
115A ASP 3.3 9.2 + - - +
116A SER 3.0 9.0 + - - +
118A LEU* 1.3 79.6 - - - +
120A VAL* 1.3 57.5 + - + +
122A LYS* 3.6 12.2 - - - +
123A TYR* 3.0 29.5 + - - +
126A ARG* 4.3 2.6 + - - +
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 6.2 0.9 - - + -
39A PRO* 4.7 7.9 - - + -
42A GLU* 5.7 3.6 - - + -
43A PHE* 4.4 24.5 - - + -
56A VAL* 4.8 11.4 - - + +
59A GLU* 4.2 11.4 - - + +
60A LEU* 4.1 24.0 - - + +
63A GLN* 4.3 1.1 - - + -
116A SER 3.2 14.7 + - - +
117A ILE* 3.7 9.4 - - - +
118A LEU 3.1 0.4 - - - -
119A ALA* 1.3 74.4 - - + +
121A LYS* 1.3 65.4 + - - +
123A TYR* 3.5 5.9 + - + +
124A PHE* 3.0 51.7 + - + -
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Residues in contact with LYS 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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59A GLU* 3.6 24.1 + - + +
63A GLN* 3.6 26.9 - - - +
117A ILE* 3.1 25.5 + - - +
118A LEU* 3.1 10.9 + - + +
120A VAL* 1.3 77.0 - - - +
122A LYS* 1.3 63.2 + - - +
124A PHE* 3.0 11.1 + - - +
125A ARG* 3.0 36.8 + - - +
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Residues in contact with LYS 122 (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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118A LEU* 2.8 54.1 + - + +
119A ALA* 3.6 9.9 - - - +
121A LYS* 1.3 71.8 - - - +
123A TYR* 1.3 65.2 + - - +
125A ARG* 2.8 39.2 + - - +
126A ARG* 3.1 29.0 + - - +
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Residues in contact with TYR 123 (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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36A PHE* 3.6 25.4 - - + -
38A PHE* 3.3 49.1 - + + -
39A PRO* 4.1 9.9 - - + -
119A ALA 3.0 15.2 + - - +
120A VAL* 3.5 4.7 - - + +
122A LYS* 1.3 77.3 - - - +
124A PHE* 1.3 92.9 + + - +
126A ARG* 3.1 34.7 - - - +
127A ILE* 3.2 27.7 + - + +
147A GLU* 2.9 23.5 + - - +
148A ILE* 4.6 2.0 - - + +
151A SER* 2.6 29.0 + - - -
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Residues in contact with PHE 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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60A LEU* 3.8 16.2 - - + -
63A GLN* 3.4 42.4 - - + +
64A ILE* 3.6 40.2 - - + -
67A LEU* 4.5 12.1 - - + -
120A VAL* 3.0 35.7 + - + +
121A LYS 3.0 9.5 + - - +
123A TYR* 1.3 98.8 - + - +
125A ARG* 1.3 60.8 + - - +
126A ARG 3.3 0.2 - - - -
127A ILE* 3.4 15.4 + - + +
128A THR* 3.2 26.6 + - + +
148A ILE* 4.0 18.2 - - + -
151A SER* 6.1 0.2 - - - -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.4 13.7 - - - +
121A LYS* 3.0 35.8 + - - +
122A LYS* 2.8 28.6 + - - +
124A PHE* 1.3 75.0 - - - +
126A ARG* 1.3 61.3 + - - +
127A ILE 3.0 1.3 - - - -
128A THR* 3.4 8.7 + - - +
129A LEU* 2.8 43.2 + - + +
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Residues in contact with ARG 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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34A HIS* 6.0 4.0 - - + -
36A PHE* 2.1 56.6 + - + +
37A GLY* 3.3 21.6 + - - -
39A PRO* 5.2 2.2 - - - +
119A ALA* 4.3 4.0 + - - +
122A LYS* 3.1 23.3 + - - +
123A TYR* 3.1 41.8 - - - +
125A ARG* 1.3 75.9 - - - +
127A ILE* 1.3 57.6 + - - +
129A LEU* 3.5 12.7 - - + +
130A TYR* 3.0 27.7 + - - +
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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
----------------------------------------------------------
36A PHE* 3.8 22.4 - - + -
67A LEU* 4.4 12.1 - - + -
123A TYR* 3.2 42.1 + - + +
124A PHE* 3.5 17.3 - - + +
125A ARG 3.0 0.6 - - - -
126A ARG* 1.3 77.0 - - - +
128A THR* 1.3 60.5 + - - +
130A TYR* 3.1 5.0 - - - +
131A LEU* 3.0 31.6 + - + +
144A VAL* 4.0 29.8 - - + -
147A GLU* 4.5 7.6 - - + -
148A ILE* 4.0 20.6 - - + -
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Residues in contact with THR 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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67A LEU* 4.4 19.7 - - + -
124A PHE* 3.2 14.6 + - + +
125A ARG* 3.2 12.9 + - - +
127A ILE* 1.3 74.6 - - - +
129A LEU* 1.3 64.4 + - - +
131A LEU* 3.0 10.3 + - + +
132A THR* 2.6 39.4 + - - -
136A TYR* 4.3 9.5 + - - +
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Residues in contact with LEU 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 ARG* 2.8 30.4 + - + +
126A ARG* 3.5 12.6 - - + +
128A THR* 1.3 82.5 + - - +
130A TYR* 1.3 64.7 + - - +
132A THR* 3.2 7.8 + - - +
133A GLU* 2.9 29.8 + - + +
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Residues in contact with TYR 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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32A ASP* 2.6 32.6 + - - +
34A HIS* 3.9 22.0 - + + -
36A PHE* 3.5 24.5 - + + -
126A ARG 3.0 12.4 + - - +
127A ILE 3.1 8.7 - - - +
129A LEU* 1.3 80.4 - - - +
131A LEU* 1.3 67.3 + - - +
133A GLU* 3.1 9.9 + - + +
134A LYS* 3.0 49.3 + - + +
140A ALA* 3.6 37.7 - - + -
143A VAL* 3.6 19.9 - - + +
144A VAL* 4.1 10.1 - - + -
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Residues in contact with LEU 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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67A LEU* 4.4 10.5 - - + -
127A ILE* 3.0 23.6 + - + +
128A THR* 3.0 11.2 + - + +
130A TYR* 1.3 77.7 - - + +
132A THR* 1.3 58.7 + - - +
134A LYS* 3.5 2.3 + - - +
135A LYS 3.2 1.9 + - - -
136A TYR* 2.6 71.4 + - + +
140A ALA* 4.0 26.9 - - + +
141A TRP* 4.2 28.9 - - + +
144A VAL* 4.0 26.5 - - + -
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Residues in contact with THR 132 (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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128A THR* 2.6 21.6 + - - -
129A LEU* 3.4 10.8 - - - +
131A LEU* 1.3 74.4 - - - +
133A GLU* 1.3 68.0 + - - +
135A LYS* 2.8 19.1 + - - +
136A TYR* 3.8 22.0 + - + -
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Residues in contact with GLU 133 (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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129A LEU* 2.9 19.9 + - + +
130A TYR* 3.1 13.0 - - + +
132A THR* 1.3 76.8 - - - +
134A LYS* 1.3 63.9 + - + +
135A LYS* 3.2 19.4 + - - +
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Residues in contact with LYS 134 (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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31A MET 3.7 15.6 + - - -
32A ASP* 3.5 27.4 + - - +
130A TYR* 3.0 52.4 + - + +
131A LEU 4.2 0.9 - - - +
133A GLU* 1.3 81.0 - - + +
135A LYS* 1.3 72.8 + - - +
136A TYR 3.0 1.1 + - - -
137A SER* 3.1 20.3 + - - +
140A ALA* 3.7 19.7 - - + -
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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