Contacts of the helix formed by residues 131 - 144 (chain A) in PDB entry 1WUR
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 GLY 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA 2.9 16.9 + - - -
89A PHE* 3.7 10.0 - - - -
130A LEU* 1.3 77.2 - - - +
132A LEU* 1.3 66.6 + - - +
133A SER 3.3 2.9 - - - -
134A LYS* 3.0 18.7 + - - +
135A PHE* 3.9 1.4 + - - -
825A 8DG 3.4 32.8 - - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.6 2.7 - - + -
99A VAL* 3.8 27.2 - - + +
123A TYR* 6.1 0.2 - - - +
130A LEU 3.2 3.5 + - - +
131A GLY* 1.3 69.8 - - - -
133A SER* 1.3 62.9 + - - +
135A PHE* 3.2 28.1 + - + +
136A ALA 4.0 1.4 + - - -
825A 8DG 3.1 41.1 + - + +
149E GLN* 5.1 1.1 - - + +
150E GLU* 4.1 7.2 - - - +
177E HIS* 3.4 44.4 - - + +
180E MET* 3.7 21.3 - - + +
192E THR* 3.5 24.0 - - + +
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Residues in contact with SER 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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132A LEU* 1.3 77.8 - - - +
134A LYS* 1.3 61.5 + - - +
136A ALA* 3.0 16.2 + - - +
137A ARG* 3.1 9.5 + - - +
825A 8DG 2.5 62.7 + - - +
179E CYS 5.4 0.4 - - - -
180E MET* 3.9 27.5 - - - -
185E VAL* 3.6 18.2 - - - +
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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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83A VAL 3.5 13.4 + - - +
84A VAL* 3.2 34.0 + - + +
85A GLY* 5.0 2.0 - - - -
87A ALA* 3.5 12.8 - - + -
130A LEU* 3.7 22.0 - - + -
131A GLY 3.0 11.1 + - - +
133A SER* 1.3 75.7 + - - +
135A PHE* 1.3 59.7 + - - +
137A ARG* 3.7 17.1 - - - +
138A ILE* 2.9 34.7 + - - +
825A 8DG 3.0 70.4 + - - +
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Residues in contact with PHE 135 (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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99A VAL* 3.8 30.5 - - + -
102A VAL* 5.2 1.1 - - + -
121A ILE* 3.7 27.0 - - + +
123A TYR* 3.3 34.3 - + - -
130A LEU* 3.7 43.1 - - + -
131A GLY 4.0 3.6 - - - -
132A LEU* 3.4 22.4 - - + +
133A SER 3.1 0.8 - - - -
134A LYS* 1.3 78.0 - - - +
136A ALA* 1.3 57.8 + - - +
138A ILE* 3.4 6.0 + - - +
139A VAL* 3.0 34.0 + - - +
160A ILE* 3.7 40.2 - - + -
164A LEU* 4.5 0.4 - - + -
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Residues in contact with ALA 136 (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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102A VAL* 3.9 17.4 - - + +
132A LEU 4.0 0.4 + - - -
133A SER 3.0 11.9 + - - +
135A PHE* 1.3 78.1 - - - +
137A ARG* 1.3 58.8 - - - +
139A VAL* 3.3 3.2 + - - +
140A ASP* 3.0 33.6 + - - -
180E MET* 4.5 8.5 - - + +
185E VAL* 3.9 13.9 - - + -
187E LYS* 3.7 31.5 - - + -
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Residues in contact with ARG 137 (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 GLN* 5.1 2.6 + - - +
83A VAL* 3.5 37.2 - - + +
133A SER 3.1 5.1 + - - +
134A LYS* 3.7 17.2 - - - +
136A ALA* 1.3 77.5 - - - +
138A ILE* 1.3 59.8 + - - +
140A ASP* 3.5 7.9 + - - +
141A MET* 3.1 22.5 + - - +
825A 8DG 2.8 42.9 + - - -
184E GLY* 3.7 21.8 - - - -
185E VAL* 3.3 21.2 - - + +
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Residues in contact with ILE 138 (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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80A LEU* 4.0 21.8 - - + -
83A VAL* 4.1 11.0 - - + -
84A VAL* 4.4 10.8 - - + -
130A LEU* 4.2 20.4 - - + -
134A LYS 2.9 21.2 + - - +
135A PHE* 3.7 6.1 - - - +
137A ARG* 1.3 74.4 - - - +
139A VAL* 1.3 67.1 + - - +
141A MET* 3.1 11.9 + - - +
142A PHE* 3.3 24.8 + - + -
156A ILE* 4.3 17.3 - - + +
159A ALA* 3.8 25.1 - - + -
160A ILE* 4.2 19.1 - - + +
163A VAL* 4.9 2.0 - - + -
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Residues in contact with VAL 139 (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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102A VAL* 4.1 18.8 - - + -
103A GLU 4.6 0.2 - - - +
104A PHE* 3.7 30.3 - - + -
119A VAL* 3.8 26.0 - - + -
121A ILE* 4.2 8.7 - - + -
135A PHE 3.0 21.2 + - - +
136A ALA* 3.4 8.7 - - - +
138A ILE* 1.3 77.3 - - - +
140A ASP* 1.3 63.8 + - - +
142A PHE* 3.3 2.1 + - - +
143A ALA* 2.8 30.6 + - + +
152A LEU* 4.6 1.8 - - + +
156A ILE* 4.0 24.2 - - + -
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Residues in contact with ASP 140 (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 GLN* 4.4 3.3 - - - +
103A GLU 4.5 0.2 - - - +
104A PHE* 5.1 2.9 - - - -
105A TYR 5.6 0.9 + - - -
136A ALA 3.0 15.8 + - - +
137A ARG* 3.9 7.4 - - - +
138A ILE 3.3 0.2 - - - -
139A VAL* 1.3 78.2 - - - +
141A MET* 1.3 61.3 + - - +
143A ALA* 4.3 5.2 - - - +
144A ARG* 3.0 72.1 + - - +
185E VAL* 5.2 6.8 - - - +
187E LYS* 2.8 36.8 + - - -
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Residues in contact with MET 141 (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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75A GLY* 3.1 25.0 - - - +
78A GLN* 3.3 40.1 + - + +
80A LEU* 4.0 30.3 - - + +
83A VAL* 3.9 21.8 - - + -
137A ARG 3.1 15.4 + - - +
138A ILE* 3.1 10.5 + - - +
140A ASP* 1.3 77.4 - - - +
142A PHE* 1.3 84.1 + - + +
145A ARG* 3.0 37.8 + - - +
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Residues in contact with PHE 142 (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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80A LEU* 4.9 2.0 - - + -
138A ILE* 3.3 31.5 + - + +
139A VAL 4.1 0.9 - - - +
141A MET* 1.3 101.8 - - + +
143A ALA* 1.3 64.0 + - - +
144A ARG 3.4 0.4 - - - -
145A ARG* 3.7 33.0 - - - +
147A GLN* 3.0 30.2 + - - +
152A LEU* 3.7 16.8 - - + -
155A GLN* 3.5 48.9 - - + +
156A ILE* 4.4 5.2 - - + -
159A ALA* 3.6 27.8 - - + -
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Residues in contact with ALA 143 (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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104A PHE* 4.2 24.0 - - + -
105A TYR 3.4 19.7 - - - +
106A SER* 2.8 30.5 + - - -
139A VAL* 2.8 21.1 + - + +
140A ASP* 4.1 6.3 - - - +
142A PHE* 1.3 76.3 - - - +
144A ARG* 1.3 55.6 + - + +
145A ARG 2.8 13.7 + - - +
152A LEU* 3.8 9.6 - - + +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.4 51.1 - - + +
72A LEU* 3.0 28.7 - - + +
73A THR* 3.3 4.3 - - - -
74A ARG* 4.0 19.2 - - - +
75A GLY* 3.0 29.0 + - - +
78A GLN* 5.6 0.9 - - - +
105A TYR 4.8 7.2 - - - +
140A ASP* 3.0 55.5 + - - +
142A PHE 3.4 0.4 - - - -
143A ALA* 1.3 73.2 - - + +
145A ARG* 1.3 64.3 + - - +
187E LYS* 5.3 2.6 - - - +
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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