Contacts of the helix formed by residues 131 - 147 (chain A) in PDB entry 1WZV
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 ASN 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU* 2.8 31.3 + - + +
130A GLN* 1.3 77.7 - - + +
132A PRO* 1.4 60.7 - - - +
133A GLU* 3.5 8.0 + - - +
134A LEU* 3.1 35.0 + - + +
135A PHE 3.0 22.5 + - - -
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Residues in contact with PRO 132 (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 LEU* 3.4 28.2 - - + +
129A THR 4.1 7.2 - - - +
130A GLN 3.9 4.7 - - - +
131A ASN* 1.4 86.3 - - - +
133A GLU* 1.3 60.4 + - - +
135A PHE* 3.6 8.2 - - + +
136A ARG* 3.0 26.7 + - - +
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Residues in contact with GLU 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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131A ASN* 3.2 6.5 + - - +
132A PRO* 1.3 78.8 - - - +
134A LEU* 1.3 61.1 + - - +
136A ARG* 3.0 42.1 + - - +
137A LYS* 2.9 56.7 + - - +
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Residues in contact with LEU 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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127A LEU* 3.7 21.3 - - + -
131A ASN* 3.1 34.4 + - + +
133A GLU* 1.3 72.2 - - - +
135A PHE* 1.3 65.3 + - - +
137A LYS* 3.4 16.6 + - + +
138A ASN* 3.0 40.6 + - - +
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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
----------------------------------------------------------
44A PRO* 5.5 2.5 - - + -
45A TYR* 3.3 32.5 - + - -
74A TYR* 3.7 27.4 - + - -
76A PRO* 3.7 19.1 - - + -
114A PRO* 6.0 1.6 - - + -
124A LEU* 3.6 35.2 - - + -
127A LEU* 3.9 16.2 - - + +
128A LEU* 3.7 38.8 - - + -
131A ASN 3.0 15.0 + - - +
132A PRO 3.6 8.7 - - - +
134A LEU* 1.3 76.4 - - - +
136A ARG* 1.3 61.5 + - + +
138A ASN* 3.2 3.9 + - - +
139A ALA* 2.9 33.7 + - + +
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Residues in contact with ARG 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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43A PRO* 4.8 9.6 - - - +
44A PRO* 3.8 24.9 - - + +
132A PRO 3.0 15.3 + - - +
133A GLU* 3.0 41.4 + - - +
135A PHE* 1.3 82.1 - - + +
137A LYS* 1.3 68.3 + - - +
139A ALA* 4.5 3.1 - - - +
140A GLU* 2.9 72.5 + - - +
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Residues in contact with LYS 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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133A GLU* 2.9 52.7 + - - +
134A LEU* 3.7 20.4 - - + +
136A ARG* 1.3 87.6 - - - +
138A ASN* 1.3 64.5 + - - +
140A GLU* 3.7 9.0 - - - +
141A GLU* 3.1 26.1 + - - +
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Residues in contact with ASN 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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74A TYR* 3.1 36.4 + - + +
127A LEU* 3.5 18.2 - - - +
134A LEU* 3.0 31.3 + - - +
135A PHE 3.6 5.4 - - - +
137A LYS* 1.3 76.2 - - - +
139A ALA* 1.3 61.8 + - - +
141A GLU* 3.4 9.9 + - - +
142A PHE* 3.0 24.3 + - - +
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Residues in contact with ALA 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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44A PRO* 3.7 16.8 - - + -
45A TYR* 3.9 19.3 - - + +
74A TYR* 3.5 25.9 - - + +
135A PHE* 2.9 23.6 + - + +
138A ASN* 1.3 77.5 - - - +
140A GLU* 1.3 52.1 + - - +
142A PHE* 3.4 1.4 + - - +
143A THR* 2.6 42.2 + - - -
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Residues in contact with GLU 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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44A PRO* 3.4 15.7 - - + +
47A LEU* 4.1 24.8 - - + +
136A ARG* 2.9 49.8 + - - +
137A LYS* 3.7 8.5 - - - +
139A ALA* 1.3 74.6 - - - +
141A GLU* 1.3 59.3 + - - +
143A THR* 3.6 2.3 - - - -
144A LEU* 2.8 48.1 + - + +
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Residues in contact with GLU 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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137A LYS 3.1 17.5 + - - +
138A ASN* 3.7 10.1 - - - +
139A ALA 3.4 0.2 - - - -
140A GLU* 1.3 76.7 + - - +
142A PHE* 1.3 58.0 + - - +
144A LEU* 3.5 6.0 + - - +
145A ARG* 3.0 40.2 + - + +
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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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72A LYS* 3.6 32.7 - - + +
73A ILE* 3.7 17.5 - - - -
74A TYR* 3.5 41.7 - + + -
121A ARG* 5.8 3.1 - - - -
138A ASN 3.0 16.8 + - - +
139A ALA 3.8 0.4 - - - +
141A GLU* 1.3 74.6 - - - +
143A THR* 1.3 60.8 + - - +
145A ARG* 3.8 4.9 - - - +
146A PHE* 2.9 57.5 + + - +
147A GLY 4.1 0.2 + - - -
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Residues in contact with THR 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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44A PRO* 3.6 23.0 + - - +
45A TYR* 3.8 22.2 - - - -
47A LEU* 4.3 4.0 - - + -
48A LYS* 3.2 37.0 - - + +
50A PHE* 4.0 17.4 - - + -
73A ILE* 5.6 0.6 - - - +
74A TYR 5.7 1.2 + - - -
139A ALA 2.6 28.1 + - - -
140A GLU* 3.6 5.4 - - - -
142A PHE* 1.3 74.0 - - - +
144A LEU* 1.3 58.8 + - - +
147A GLY* 2.8 27.7 + - - +
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Residues in contact with LEU 144 (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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47A LEU* 3.7 33.7 - - + -
48A LYS* 4.1 25.2 + - - +
140A GLU* 2.8 40.7 + - + +
141A GLU* 4.1 5.4 - - - +
143A THR* 1.3 73.6 - - - +
145A ARG* 1.3 60.5 + - - +
147A GLY 4.6 2.1 + - - +
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Residues in contact with ARG 145 (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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141A GLU* 3.0 27.9 + - + +
142A PHE* 3.8 5.8 - - - +
144A LEU* 1.3 79.2 - - - +
146A PHE* 1.3 101.1 + - + +
147A GLY 5.0 0.9 - - - +
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Residues in contact with PHE 146 (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 THR* 3.5 14.2 - - - +
72A LYS* 4.0 33.4 - - + +
142A PHE* 2.9 52.7 + + + +
145A ARG* 1.3 124.0 - - + +
147A GLY* 1.3 68.0 + - - +
148A VAL* 5.0 0.9 - - - +
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Residues in contact with GLY 147 (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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48A LYS* 3.7 21.1 + - - +
49A ALA 3.9 3.6 - - - -
50A PHE* 4.5 6.5 - - - -
71A THR* 4.1 6.1 - - - -
72A LYS 4.9 0.6 + - - -
142A PHE 4.1 0.6 + - - -
143A THR* 2.8 21.3 + - - +
144A LEU 5.0 1.6 - - - +
145A ARG 3.7 1.6 - - - +
146A PHE* 1.3 82.6 - - - +
148A VAL* 1.3 64.4 + - - -
149A ASP* 3.9 1.2 + - - +
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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