Contacts of the helix formed by residues 113 - 130 (chain A) in PDB entry 1UZL
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 LEU 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 2.9 29.6 + - + +
112A ASN* 1.3 77.7 - - - +
114A THR* 1.3 61.5 + - - +
115A GLY 3.3 0.7 - - - -
116A ALA* 3.0 6.2 + - - +
117A PHE* 2.9 25.3 + - - +
155A ALA 4.7 1.6 - - - +
156A SER* 4.2 19.3 - - - +
159A GLY* 3.4 21.1 - - - +
160A VAL* 3.4 34.3 - - + +
163A MET* 4.4 11.8 - - + +
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Residues in contact with THR 114 (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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109A ILE* 3.0 16.1 + - - +
110A ASN* 3.5 18.1 + - - +
113A LEU* 1.3 78.8 - - - +
115A GLY* 1.3 56.6 + - - +
117A PHE* 3.2 15.4 + - + +
118A ARG* 2.8 61.5 + - + +
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.3 30.0 - - - +
87A SER* 5.1 0.7 - - - -
110A ASN 2.8 12.5 + - - -
111A ALA 3.6 15.6 + - - -
113A LEU 3.3 0.6 - - - -
114A THR* 1.3 75.4 - - - +
116A ALA* 1.3 61.4 + - - +
118A ARG* 3.3 2.9 + - - +
119A VAL* 3.2 28.3 + - - +
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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
----------------------------------------------------------
87A SER* 3.8 20.6 - - - +
111A ALA 4.2 1.0 + - - -
112A ASN 3.5 18.6 + - - +
113A LEU 3.0 11.1 + - - +
115A GLY* 1.3 76.2 - - - +
117A PHE* 1.3 62.8 + - - +
119A VAL* 3.5 3.3 - - - +
120A ALA* 3.1 25.1 + - - +
137A PHE* 3.9 8.5 - - + -
160A VAL* 4.1 11.2 - - + -
163A MET* 3.8 16.6 - - + +
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Residues in contact with PHE 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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113A LEU* 2.9 10.6 + - + +
114A THR* 3.4 21.3 - - + +
116A ALA* 1.3 76.8 - - - +
118A ARG* 1.3 67.5 + - + +
120A ALA* 3.7 2.4 - - + +
121A GLN* 2.8 63.3 + - + +
163A MET* 3.5 27.4 - - + -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL 3.0 26.9 + - - +
63A THR* 3.3 20.4 + - - +
64A ASP 4.2 0.7 - - - -
65A SER* 3.1 39.7 + - - +
68A VAL* 4.0 13.2 - - + +
110A ASN* 3.1 42.2 + - - +
114A THR* 2.8 33.2 + - - +
115A GLY 3.3 14.5 + - - +
117A PHE* 1.3 87.0 - - + +
119A VAL* 1.3 63.2 + - - +
121A GLN* 3.5 4.4 + - - +
122A ARG* 3.1 24.4 + - - +
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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
----------------------------------------------------------
21A THR* 4.1 18.2 - - + -
60A CYS* 5.6 1.8 - - - -
62A VAL* 4.2 9.9 - - + -
68A VAL* 4.0 28.9 - - + -
72A PHE* 3.6 16.4 - - + -
85A LEU* 3.7 22.2 - - + -
87A SER* 3.5 26.9 - - - +
115A GLY 3.2 11.4 + - - +
116A ALA 3.5 8.5 - - - +
118A ARG* 1.3 75.6 - - - +
120A ALA* 1.3 64.9 + - - +
122A ARG* 3.5 0.7 + - - +
123A ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 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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85A LEU* 3.9 9.4 - - - -
116A ALA 3.1 18.7 + - - +
117A PHE* 3.7 6.3 - - + +
119A VAL* 1.3 78.8 - - - +
121A GLN* 1.3 61.1 + - - +
123A ALA 3.3 1.2 + - - -
124A SER* 3.1 20.0 + - - -
135A MET* 3.4 31.0 - - - +
137A PHE* 3.9 14.1 - - + -
163A MET* 4.4 0.2 - - + -
167A ILE* 4.1 13.9 - - + -
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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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117A PHE* 2.8 52.4 + - + +
118A ARG* 3.9 3.9 - - - +
120A ALA* 1.3 74.1 - - - +
122A ARG* 1.3 69.7 + - - +
124A SER* 2.9 26.1 + - - +
125A ARG* 4.4 15.3 + - - +
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Residues in contact with ARG 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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68A VAL* 3.9 16.8 - - + +
69A ASP* 3.0 29.1 + - - +
72A PHE* 3.4 45.3 - - + +
73A THR* 3.1 30.3 + - - +
76A GLU* 6.0 1.2 - - - +
118A ARG 3.1 17.5 + - - +
119A VAL 3.8 4.0 - - - +
121A GLN* 1.3 84.8 + - - +
123A ALA* 1.3 61.0 + - - +
125A ARG* 3.5 30.9 + - - +
126A SER* 5.4 7.2 + - - -
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Residues in contact with ALA 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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72A PHE* 3.6 22.0 - - + -
82A VAL* 4.9 2.7 - - + +
85A LEU* 4.2 9.2 - - + -
119A VAL 3.1 18.0 + - - +
120A ALA 3.7 4.5 - - - +
121A GLN 3.2 0.2 - - - -
122A ARG* 1.3 76.7 - - - +
124A SER* 1.3 64.3 + - - +
125A ARG 3.4 0.9 + - - -
126A SER* 3.7 7.4 + - - -
127A MET* 3.4 47.6 + - + +
135A MET* 4.4 1.1 - - + -
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Residues in contact with SER 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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120A ALA 3.1 15.5 + - - -
121A GLN* 2.9 22.4 + - - +
123A ALA* 1.3 77.4 - - - +
125A ARG* 1.3 68.4 + - - +
127A MET* 3.1 4.4 + - - +
128A GLN* 3.0 33.9 + - - +
135A MET* 4.2 14.6 - - - -
171A LEU* 4.2 14.8 - - - -
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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
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69A ASP* 5.4 0.4 + - - -
121A GLN* 4.4 15.6 + - - +
122A ARG* 3.5 46.5 + - - +
123A ALA 3.5 0.8 - - - -
124A SER* 1.3 80.5 + - - +
126A SER* 1.3 58.9 + - - +
128A GLN* 3.3 10.8 + - - +
129A ARG* 2.8 45.7 + - - +
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Residues in contact with SER 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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81A PRO* 3.3 30.1 - - - +
82A VAL 4.8 6.7 + - - -
122A ARG* 5.4 7.3 + - - -
123A ALA 3.7 8.2 + - - -
125A ARG* 1.3 79.8 - - - +
127A MET* 1.3 56.5 + - - +
129A ARG* 3.5 23.2 + - - +
130A ASN* 2.7 41.4 + - - +
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Residues in contact with MET 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* 3.6 23.6 - - + +
83A GLU 3.4 25.4 - - - +
85A LEU* 4.0 12.3 - - + +
123A ALA* 3.4 24.8 + - + +
124A SER 3.1 8.5 + - - +
126A SER* 1.3 75.0 - - - +
128A GLN* 1.3 61.4 + - - +
130A ASN 3.3 0.3 + - - -
131A LYS 2.9 22.7 + - - -
132A PHE 3.0 29.6 + - - +
133A GLY* 3.8 9.0 - - - -
134A ARG 3.9 13.7 - - - +
135A MET* 3.8 29.8 - - + -
176A VAL* 3.5 16.7 - - + +
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Residues in contact with GLN 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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124A SER* 3.0 32.5 + - - +
125A ARG* 3.8 8.9 - - - +
127A MET* 1.3 73.7 - - - +
129A ARG* 1.3 65.0 + - - +
131A LYS* 3.1 32.2 + - - +
170A GLU* 4.9 4.6 + - - +
171A LEU* 3.5 37.1 - - + +
174A ALA* 4.5 11.0 - - + +
176A VAL* 3.9 9.4 - - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 2.8 24.8 + - - +
126A SER* 3.5 34.4 + - - +
128A GLN* 1.3 79.5 - - - +
130A ASN* 1.3 69.0 + - - +
131A LYS* 3.4 9.5 + - - +
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Residues in contact with ASN 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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81A PRO* 4.9 9.3 - - - +
83A GLU* 6.5 1.6 - - + -
126A SER* 2.7 43.9 + - - +
127A MET 4.3 1.3 - - - +
128A GLN 3.2 0.4 - - - -
129A ARG* 1.3 88.6 - - - +
131A LYS* 1.3 71.1 + - - +
132A PHE* 3.1 11.8 + - + +
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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
------------------------------------------------------------
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