Contacts of the helix formed by residues 130 - 143 (chain A) in PDB entry 4WUR
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 ILE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU 3.3 19.5 - - - +
72A TYR* 3.5 16.4 - - - +
73A GLY* 4.9 5.4 - - - +
74A PRO* 6.2 0.9 - - + -
128A PHE* 3.4 1.6 - - - +
129A VAL* 1.3 79.5 - - + +
131A PRO* 1.4 56.2 - - + +
132A ALA* 4.2 0.4 - - + -
133A LEU* 3.0 20.0 + - + +
134A GLN* 2.8 34.3 + - - +
155A TYR* 3.3 34.3 - - + +
176A LYS* 3.3 38.1 - - + -
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Residues in contact with PRO 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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70A GLU 3.4 22.4 - - - +
71A LEU* 3.4 27.8 - - + +
73A GLY 5.5 0.7 - - - +
129A VAL 3.4 8.9 - - - +
130A ILE* 1.4 80.7 - - + +
132A ALA* 1.3 62.4 + - - +
134A GLN* 3.1 6.7 + - + +
135A HIS* 2.9 27.7 + - - +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 2.9 35.0 + - + +
72A TYR* 3.4 35.7 - - + -
130A ILE* 4.2 1.6 - - + -
131A PRO* 1.3 76.9 - - - +
133A LEU* 1.3 56.1 + - - +
135A HIS* 3.8 5.4 - - - +
136A ALA* 3.0 30.0 + - - +
151A LEU* 3.6 6.3 - - + +
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Residues in contact with LEU 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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128A PHE* 3.4 36.1 - - + -
130A ILE* 3.0 21.1 + - + +
132A ALA* 1.3 75.6 - - - +
134A GLN* 1.3 66.6 + - - +
136A ALA* 3.8 0.3 - - - +
137A PHE* 3.1 24.3 + - - +
148A PHE* 3.7 23.8 - - + -
151A LEU* 4.1 15.7 - - + +
152A ILE* 4.7 6.5 - - + -
155A TYR* 4.3 28.5 - - + -
173A VAL* 4.9 3.6 - - + +
176A LYS* 3.7 25.4 - - + -
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Residues in contact with GLN 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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126A ILE 5.2 0.8 + - - -
127A LYS* 3.4 16.0 - - - +
128A PHE* 2.5 51.1 + - - +
130A ILE 2.8 12.9 + - - +
131A PRO* 3.1 10.7 + - + +
133A LEU* 1.3 77.9 - - - +
135A HIS* 1.3 58.2 + - - +
137A PHE* 3.2 13.1 - - - +
138A MET* 3.0 60.1 + - + +
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Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 6.4 0.2 - - + -
131A PRO 2.9 16.5 + - - +
132A ALA* 3.8 6.0 + - - +
134A GLN* 1.3 78.1 - - - +
136A ALA* 1.3 59.4 + - - +
138A MET* 3.2 12.3 + - + +
139A LYS* 3.0 47.0 + - + +
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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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132A ALA 3.0 18.6 + - - +
133A LEU 3.8 3.6 - - - +
135A HIS* 1.3 76.8 - - - +
137A PHE* 1.3 53.3 - - - +
139A LYS* 3.3 10.2 - - - +
140A HIS* 2.9 24.8 + - - -
144A ASP 4.3 0.3 - - - +
147A ASP* 3.7 22.4 - - + -
148A PHE* 3.4 23.3 + - + +
151A LEU* 3.5 22.7 - - + -
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Residues in contact with PHE 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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120A LEU* 4.6 17.3 - - + -
121A ASP* 5.2 2.5 - - - -
123A LEU 5.9 0.4 - - - -
126A ILE* 4.1 36.8 - - + -
128A PHE* 3.5 23.8 - + + -
133A LEU 3.1 12.0 + - - +
134A GLN* 3.2 24.2 - - - +
136A ALA* 1.3 77.4 - - - +
138A MET* 1.3 58.9 - - - +
139A LYS 3.2 0.2 - - - -
140A HIS* 3.0 17.0 + + - +
141A LYS* 2.9 48.1 + - + +
148A PHE* 3.5 38.6 - + + -
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Residues in contact with MET 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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134A GLN* 3.0 43.2 + - + +
135A HIS* 3.2 15.9 + - + +
137A PHE* 1.3 75.4 - - - +
139A LYS* 1.3 58.8 + - + +
141A LYS* 3.3 23.4 + - + +
142A GLY* 3.0 22.0 + - - -
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Residues in contact with LYS 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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87A LYS* 5.6 0.2 - - - +
135A HIS* 3.0 43.0 + - + +
136A ALA* 3.3 11.0 - - - +
138A MET* 1.3 74.5 - - - +
140A HIS* 1.3 57.9 + - - +
142A GLY* 2.8 20.0 + - - +
143A GLY 3.1 0.5 + - - -
144A ASP* 3.0 52.0 + - + +
147A ASP* 3.0 34.3 + - + +
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Residues in contact with HIS 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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95A MET* 4.5 3.4 - - + -
102A ARG* 3.5 26.9 + - + -
117A ILE* 3.6 27.0 - - + +
120A LEU* 6.3 0.2 - - - +
121A ASP* 2.9 30.2 + - - -
136A ALA 2.9 15.3 + - - +
137A PHE* 3.0 22.9 + + - +
139A LYS* 1.3 77.2 - - - +
141A LYS* 1.3 66.0 + - + +
142A GLY 3.1 0.2 - - - -
143A GLY* 3.3 9.5 + - - -
144A ASP 3.2 10.1 + - - +
145A SER* 2.6 33.3 + - - -
148A PHE* 3.7 29.4 - + + -
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Residues in contact with LYS 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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121A ASP* 5.5 2.7 - - - +
137A PHE* 2.9 50.2 + - + +
138A MET* 3.6 23.6 - - + +
140A HIS* 1.3 83.1 - - + +
142A GLY* 1.3 63.0 + - - +
143A GLY 3.2 0.2 - - - -
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Residues in contact with GLY 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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138A MET 3.0 9.3 + - - -
139A LYS* 2.8 12.1 + - - -
141A LYS* 1.3 80.0 - - - +
143A GLY* 1.3 57.7 + - - +
144A ASP 3.6 1.1 - - - -
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Residues in contact with GLY 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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102A ARG* 3.0 36.0 + - - -
139A LYS 3.1 0.6 + - - -
140A HIS 3.3 3.8 + - - -
141A LYS 3.2 3.8 - - - -
142A GLY* 1.3 81.3 - - - +
144A ASP* 1.3 58.6 + - - +
145A SER 4.0 0.2 + - - -
401A IPA 5.1 2.9 - - - +
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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