Contacts of the helix formed by residues 120 - 131 (chain A) in PDB entry 4UAL
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 CYS 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU 5.2 2.7 - - - -
118A THR* 3.3 16.5 + - - -
119A ALA* 1.3 67.1 - - - +
121A PHE* 1.3 58.5 + - - +
122A ARG 3.3 2.9 - - - -
123A GLU* 3.3 14.4 - - - +
124A GLU* 2.9 27.4 + - - +
199A ARG* 3.7 21.8 - - - -
220A GLY 3.3 12.4 - - - +
221A SER 3.9 4.3 - - - -
222A CYS 3.3 27.6 - - - +
223A LEU* 4.1 11.4 - - - -
504A EDO 2.9 8.9 + - - -
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Residues in contact with PHE 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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107A LEU* 4.5 5.4 - - + -
112A MET* 3.8 42.8 - - + -
113A LEU* 4.6 8.3 - - + -
116A ALA* 6.2 2.5 - - + -
119A ALA 2.9 16.2 + - - -
120A CYS* 1.3 73.8 - - - +
122A ARG* 1.3 79.5 + - + +
124A GLU* 3.4 6.0 + - - +
125A ARG* 3.0 29.6 + - - +
149A LEU* 3.7 21.8 - - + -
397A PRO* 3.8 22.9 - - + -
398A PHE* 3.7 31.2 - + - -
401A PHE* 4.1 11.0 - + + -
504A EDO 3.8 9.8 - - - -
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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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121A PHE* 1.3 93.7 - - + +
123A GLU* 1.3 69.7 + - - +
125A ARG* 3.3 9.6 + - - +
126A ASP* 2.9 50.6 + - - +
397A PRO 2.9 33.5 + - - -
398A PHE* 3.6 8.7 + - - +
399A ILE 2.8 29.8 + - - -
400A GLY* 3.4 21.5 + - - -
401A PHE* 4.2 8.6 - - - +
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Residues in contact with GLU 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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120A CYS* 3.3 25.3 - - - +
122A ARG* 1.3 82.3 + - - +
124A GLU* 1.3 65.6 + - - +
126A ASP* 4.4 2.9 - - - +
127A VAL* 2.8 30.1 + - - +
196A TYR* 4.0 22.7 - - + +
219A PHE 4.5 0.4 - - - -
222A CYS* 3.3 36.6 - - + +
223A LEU* 4.0 18.2 - - - +
224A LYS* 4.4 5.3 + - + +
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Residues in contact with GLU 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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105A LYS* 2.9 29.2 + - - +
107A LEU* 4.1 4.5 - - - +
120A CYS 2.9 16.2 + - - +
121A PHE* 3.6 5.5 - - - +
122A ARG 3.3 0.2 - - - -
123A GLU* 1.3 77.5 - - - +
125A ARG* 1.3 66.3 + - - +
127A VAL* 4.0 1.2 - - - +
128A LEU* 3.1 31.1 + - + +
151A LEU* 3.7 25.3 - - + +
219A PHE* 3.5 28.4 + - + +
220A GLY* 3.8 11.1 + - - +
501A 3FV 3.8 8.1 - - - +
504A EDO 2.9 25.9 + - - -
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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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29A THR* 5.3 0.6 + - - -
121A PHE 3.0 14.0 + - - +
122A ARG* 3.6 8.7 - - - +
123A GLU 3.2 0.2 - - - -
124A GLU* 1.3 82.4 - - - +
126A ASP* 1.3 79.3 + - - +
128A LEU* 3.3 6.1 + - - +
129A VAL* 3.0 58.1 + - + +
130A ASN* 5.3 1.4 - - - +
139A LEU* 5.3 0.2 - - + -
142A ALA* 4.4 7.0 - - + -
151A LEU* 4.5 7.2 - - + +
400A GLY 3.1 16.8 + - - -
401A PHE* 2.9 47.4 + - + +
402A THR 2.9 24.7 + - - -
403A PHE* 3.8 10.5 - - - +
411A ASP* 2.9 33.9 + - - -
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Residues in contact with ASP 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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122A ARG* 2.9 41.2 + - - +
123A GLU* 3.2 2.7 + - - +
125A ARG* 1.3 96.3 + - - +
127A VAL* 1.3 61.7 + - - +
129A VAL* 4.5 1.6 - - - +
130A ASN* 3.0 45.9 + - - +
196A TYR* 3.6 23.8 + - - +
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Residues in contact with VAL 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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123A GLU 2.8 23.6 + - - +
124A GLU 4.0 2.5 - - - +
126A ASP* 1.3 72.9 - - - +
128A LEU* 1.3 57.1 + - - +
131A GLY* 2.8 29.8 + - - -
136A ILE* 3.5 6.5 - - + +
191A ILE* 3.9 20.6 - - + -
194A LEU* 4.1 9.6 - - + -
196A TYR* 3.5 44.4 - - + -
219A PHE* 3.7 31.9 - - + -
222A CYS* 4.2 9.4 - - - -
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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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124A GLU* 3.1 29.5 + - + +
125A ARG 3.7 4.0 - - - +
127A VAL* 1.3 75.9 - - - +
129A VAL* 1.3 62.9 + - - +
131A GLY 4.2 2.8 + - - +
136A ILE* 4.2 9.1 - - + +
137A THR* 3.4 38.7 - - - +
139A LEU* 3.7 30.6 + - + +
151A LEU* 4.0 32.8 - - + -
153A MET* 4.3 16.8 - - - -
219A PHE* 3.7 22.0 - - + -
403A PHE* 5.8 0.2 - - - -
501A 3FV 6.3 0.9 - - + -
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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 ARG* 3.0 38.3 + - - +
126A ASP 3.9 3.4 - - - +
128A LEU* 1.3 79.1 - - - +
130A ASN* 1.3 72.1 + - - +
131A GLY 3.7 0.7 + - - +
139A LEU* 3.6 20.4 - - + -
403A PHE* 3.7 41.1 - - + -
411A ASP* 4.1 13.9 - - + -
412A ARG* 2.9 33.1 + - + +
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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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19A TRP* 3.5 32.2 - - + -
125A ARG* 5.3 0.8 - - - +
126A ASP* 3.0 35.2 + - - +
129A VAL* 1.3 86.9 - - - +
131A GLY* 1.3 64.6 + - - +
194A LEU* 3.3 27.7 - - + +
196A TYR* 6.4 0.7 - - + -
411A ASP* 4.7 5.8 + - - +
412A ARG* 3.6 18.4 + - - +
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Residues in contact with GLY 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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127A VAL 2.8 18.3 + - - -
128A LEU 4.2 1.9 + - - +
129A VAL 3.5 2.1 - - - +
130A ASN* 1.3 81.6 - - - +
132A ASP* 1.3 64.1 - - - -
133A CYS* 3.4 4.9 + - - +
136A ILE* 3.8 10.5 - - - -
190A SER 5.8 0.4 - - - -
191A ILE* 5.8 1.3 - - - -
194A LEU* 3.8 16.2 - - - -
412A ARG* 3.8 11.4 + - - -
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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
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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