Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 2UZ8
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 THR 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR 4.6 3.8 - - - +
60A LEU* 3.2 26.9 - - - +
62A GLY 4.6 0.2 - - - +
67A GLU* 4.4 14.8 - - - +
71A VAL* 3.7 16.8 - - + -
109A THR* 3.5 36.1 - - - +
112A ASN* 3.7 5.4 - - + +
113A PHE* 1.3 81.9 - - - +
115A LEU* 1.3 63.1 + - - +
116A ALA* 3.3 12.0 + - - +
117A ASP* 3.0 25.8 + - - +
118A ILE* 3.7 8.6 + - - +
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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
----------------------------------------------------------
10A LEU* 3.9 32.1 - - + -
48A ALA* 4.1 19.3 - - + -
49A ALA 4.3 0.4 - - - +
52A VAL* 4.0 17.9 - - + -
60A LEU* 2.8 29.5 + - + +
61A LEU* 3.7 23.8 - - + -
71A VAL* 4.7 1.1 - - + -
75A LEU* 4.1 25.1 - - + -
114A THR* 1.3 68.3 - - - +
116A ALA* 1.3 64.0 + - - +
118A ILE* 3.1 14.2 + - + -
119A LEU* 3.0 35.5 + - + +
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Residues in contact with ALA 116 (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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71A VAL* 4.2 13.3 - - - +
74A TRP* 3.5 32.6 - - + +
75A LEU* 3.9 12.8 - - + +
108A LEU* 3.4 8.2 - - + +
109A THR* 4.0 10.5 - - + -
114A THR* 3.1 13.1 + - - +
115A LEU* 1.3 79.8 - - - +
117A ASP* 1.3 60.1 + - - +
119A LEU* 4.1 0.6 - - - +
120A LEU* 3.1 26.9 + - - +
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Residues in contact with ASP 117 (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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107A TYR* 3.6 19.0 - - - +
108A LEU* 2.8 31.4 + - - +
109A THR 4.8 0.2 + - - -
112A ASN 4.0 0.7 - - - +
113A PHE* 3.6 19.6 - - + -
114A THR* 3.0 34.6 + - - +
116A ALA* 1.3 74.1 - - - +
118A ILE* 1.3 65.3 + - - +
121A TYR* 2.9 27.6 + - - +
145A TRP* 3.0 25.2 + - - -
149A ILE* 4.0 11.0 - - + -
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 17.9 - - + -
13A SER* 4.5 2.0 - - - +
14A LEU* 5.1 2.9 - - + -
60A LEU* 4.3 16.4 - - + -
113A PHE* 3.4 37.0 - - + -
114A THR 3.9 2.2 - - - +
115A LEU* 3.1 26.3 + - + +
117A ASP* 1.3 75.5 - - - +
119A LEU* 1.3 60.9 + - + +
121A TYR* 3.2 6.9 + - - +
122A TYR* 2.9 69.8 + - + +
149A ILE* 4.8 3.4 - - - -
155A ILE* 4.1 17.3 - - + -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 4.0 15.3 - - + +
7A LEU* 6.1 0.2 - - + -
10A LEU* 4.4 16.6 - - + -
44A LEU* 4.5 12.3 - - + -
45A THR* 4.1 18.2 - - + -
48A ALA* 3.8 22.0 - - + -
75A LEU* 4.0 22.7 - - + -
78A ARG* 3.0 36.5 + - + +
115A LEU* 3.0 31.3 + - + +
116A ALA 4.4 1.3 - - - +
118A ILE* 1.3 79.2 - - - +
120A LEU* 1.3 58.5 + - - +
122A TYR* 3.5 10.9 + - + +
123A GLY 3.0 12.8 + - - -
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Residues in contact with LEU 120 (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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74A TRP* 4.7 3.1 - - + +
77A TYR* 3.8 17.5 - - + -
78A ARG* 4.5 11.3 - - + +
82A VAL* 3.7 30.1 - - + -
98A LEU* 4.1 19.7 - - + -
108A LEU* 3.7 32.1 - - + -
116A ALA 3.1 19.8 + - - +
119A LEU* 1.3 75.0 - - - +
121A TYR* 1.3 60.2 + - - +
124A LEU* 2.9 39.7 + - + +
145A TRP* 3.7 22.4 - - + -
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Residues in contact with TYR 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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117A ASP 2.9 19.3 + - - +
118A ILE 3.5 1.6 - - - +
120A LEU* 1.3 75.0 - - - +
122A TYR* 1.3 92.6 + + - +
125A HIS* 2.9 36.0 + + - +
145A TRP* 3.6 11.5 - - + -
146A PHE* 3.4 46.6 - + - -
149A ILE* 3.5 18.6 - - + -
150A GLN* 3.5 28.8 + - + +
155A ILE* 3.8 21.3 - - + -
156A ARG* 3.3 33.0 - - - +
159A LEU* 3.9 16.6 - - + +
160A SER 4.6 0.2 + - - -
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 3.5 38.5 - - + +
9A LEU* 3.7 28.5 - - + +
10A LEU* 4.1 17.0 - - + -
13A SER* 2.7 25.1 + - - -
78A ARG* 4.5 0.7 - - - -
118A ILE* 2.9 37.6 + - + +
119A LEU* 3.9 5.8 - - + +
121A TYR* 1.3 99.3 - + - +
123A GLY* 1.3 60.6 + - - +
125A HIS* 3.7 14.5 + - - +
126A ARG* 4.7 1.9 + - - +
155A ILE* 2.9 29.3 + - + -
159A LEU* 3.7 14.7 - - + +
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Residues in contact with GLY 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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78A ARG* 3.6 33.4 - - - +
82A VAL* 3.7 15.9 - - - +
83A ASP* 5.2 0.2 - - - -
119A LEU 3.0 11.8 + - - -
120A LEU 3.2 2.4 + - - -
122A TYR* 1.3 78.8 - - - +
124A LEU* 1.3 58.6 + - - +
125A HIS 3.7 0.2 + - - -
126A ARG* 4.2 9.5 + - - +
127A PHE* 3.9 10.7 - - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 6.0 0.9 - - - +
82A VAL* 4.0 25.4 - - + -
91A ILE* 4.9 1.8 - - + -
94A LEU* 4.8 9.9 - - + -
95A LEU* 4.4 19.7 - - + -
98A LEU* 3.8 28.5 - - + -
120A LEU* 2.9 34.6 + - + +
121A TYR 4.3 1.3 - - - +
123A GLY* 1.3 74.3 - - - +
125A HIS* 1.3 66.8 + - - +
126A ARG 3.0 3.8 - - - -
127A PHE* 2.8 28.7 + - + -
128A ILE* 2.9 27.2 + - + +
142A VAL* 4.9 0.9 - - + -
145A TRP* 4.1 11.0 - - + -
146A PHE* 4.6 3.6 - - + -
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Residues in contact with HIS 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 TYR* 2.9 23.7 + - - +
122A TYR 3.7 10.3 - - - +
123A GLY 3.4 1.0 - - - -
124A LEU* 1.3 76.9 - - - +
126A ARG* 1.3 65.3 + - - +
129A VAL* 3.0 50.0 + - + +
146A PHE* 3.8 25.8 - + + -
159A LEU* 3.7 36.2 - - + +
160A SER* 3.0 44.4 + - - -
162A VAL* 4.9 0.4 - - + -
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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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82A VAL 5.2 4.6 + - - -
83A ASP* 6.0 2.2 - - - +
122A TYR 4.7 1.5 + - - +
123A GLY 4.2 8.4 + - - +
125A HIS* 1.3 81.3 + - - +
127A PHE* 1.3 101.4 + - + +
129A VAL* 3.1 22.2 - - - +
130A ASP* 3.8 11.1 - - - +
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Residues in contact with PHE 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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82A VAL* 4.3 13.2 - - + -
91A ILE* 3.4 54.7 - - + -
95A LEU* 5.4 1.1 - - + -
123A GLY 3.9 21.5 - - - -
124A LEU* 2.8 25.0 + - + +
126A ARG* 1.3 115.4 - - + +
128A ILE* 1.3 70.6 + - + +
129A VAL 3.3 0.4 - - - -
130A ASP* 3.2 13.8 + - - +
131A LEU* 3.6 17.2 + - + +
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Residues in contact with ILE 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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95A LEU* 4.1 25.8 - - + -
124A LEU* 2.9 26.6 + - + +
125A HIS 4.0 0.2 - - - +
127A PHE* 1.3 76.7 - - + +
129A VAL* 1.3 65.0 + - - +
130A ASP 3.1 1.2 + - - -
131A LEU* 3.2 38.8 + - + +
136A LYS* 4.9 1.7 + - + +
142A VAL* 4.3 14.4 - - + -
143A SER* 5.9 1.3 - - - +
146A PHE* 3.6 49.4 - - + -
162A VAL* 4.2 10.5 - - + +
164A PHE* 4.0 17.7 - - + -
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Residues in contact with VAL 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 HIS* 3.0 48.4 + - + +
126A ARG* 3.1 25.6 - - - +
128A ILE* 1.3 75.5 - - - +
130A ASP* 1.3 71.2 + - - +
131A LEU 4.6 2.9 - - - +
136A LYS* 5.9 1.0 + - - -
160A SER* 3.5 12.1 - - - +
162A VAL* 3.9 17.7 - - + +
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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