Contacts of the helix formed by residues 121 - 139 (chain A) in PDB entry 1WZ2
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 ASP 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR 3.7 12.9 + - - +
119A PHE 2.7 14.3 - - - +
120A GLU* 1.3 76.6 - - - +
122A PRO* 1.3 76.2 - - - +
123A ILE* 3.3 19.1 + - - +
124A ASN* 3.2 36.1 + - - +
125A ILE* 3.6 1.9 - - - +
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Residues in contact with PRO 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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87A ILE* 5.0 4.0 - - + +
88A VAL* 4.3 31.9 - - + +
91A ALA* 3.8 17.9 - - + -
92A GLU* 4.7 5.4 - - - +
120A GLU 3.3 7.6 - - - +
121A ASP* 1.3 84.5 - - - +
123A ILE* 1.3 56.8 + - + +
124A ASN 2.9 4.9 - - - -
125A ILE* 2.5 37.7 + - + +
126A VAL* 2.9 13.1 + - - +
514A LEU* 4.7 11.7 - - + -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 6.1 0.7 - - + -
121A ASP* 3.3 15.0 + - - +
122A PRO* 1.3 77.0 - - + +
124A ASN* 1.3 61.5 + - - +
125A ILE 3.3 0.2 - - - -
126A VAL* 3.6 16.4 - - + +
127A LYS* 2.9 32.6 + - + +
155A LEU* 3.1 36.3 - - + -
514A LEU* 5.1 13.7 - - + -
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 2.7 48.4 + - - +
119A PHE* 3.6 12.7 - - + -
121A ASP* 3.2 26.6 + - - +
122A PRO 2.8 0.8 + - - -
123A ILE* 1.3 80.1 + - - +
125A ILE* 1.3 61.1 + - - +
127A LYS* 3.4 23.3 - - - +
128A TYR* 3.0 24.8 + - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 4.4 2.1 - - - +
46A SER* 4.9 2.7 - - - +
87A ILE* 3.9 34.8 - - + +
90A ILE* 4.2 10.3 - - + -
91A ALA* 3.9 13.5 - - + +
105A TYR* 4.7 10.8 - - + +
119A PHE* 3.2 43.7 - - + +
121A ASP 3.6 6.7 - - - +
122A PRO* 2.5 19.8 + - + +
124A ASN* 1.3 70.0 - - - +
126A VAL* 1.3 58.3 + - + +
127A LYS 3.0 7.5 + - - -
129A PHE* 3.4 47.7 + - + +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.1 10.1 - - + +
82A ILE* 3.1 50.7 - - + -
87A ILE* 3.9 37.7 - - + -
122A PRO 2.9 16.1 + - - +
123A ILE* 3.5 16.8 + - + +
125A ILE* 1.3 75.8 - - - +
127A LYS* 1.3 57.9 + - - +
130A MET* 3.3 26.6 - - - +
151A TYR* 6.1 0.2 - - + -
514A LEU* 6.1 2.0 - - + -
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Residues in contact with LYS 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 ILE* 2.9 24.0 + - + +
124A ASN* 3.4 24.1 - - - +
125A ILE 3.0 0.4 - - - -
126A VAL* 1.3 79.0 - - - +
128A TYR* 1.3 69.1 + - - +
129A PHE 3.2 1.6 - - - -
130A MET* 3.4 3.9 + - - +
131A LYS* 3.3 23.9 + - - +
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Residues in contact with TYR 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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48A HIS* 3.9 13.7 + + - -
110A LYS 3.6 17.0 + - - -
111A VAL* 3.2 32.0 - - + +
112A PRO* 4.2 11.4 - - + +
115A ILE* 4.6 17.5 - - + -
119A PHE* 3.7 26.5 - + + -
124A ASN 3.0 16.5 + - - +
125A ILE 4.9 0.4 - - - +
127A LYS* 1.3 79.3 - - - +
129A PHE* 1.3 68.9 + + + +
131A LYS* 3.8 19.4 - - + +
132A ALA* 3.0 27.4 + - + +
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Residues in contact with PHE 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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45A LEU* 4.2 13.6 - - + +
46A SER* 3.8 5.6 - - - -
47A GLY* 3.7 45.7 - - - +
48A HIS* 3.8 33.9 - + - -
105A TYR* 3.4 39.9 - + - -
109A TYR* 4.5 2.7 - - + -
111A VAL* 4.3 2.7 - - + -
119A PHE* 4.2 6.3 - + - -
125A ILE* 3.4 33.6 + - + +
127A LYS 3.2 0.4 - - - -
128A TYR* 1.3 94.0 - + - +
130A MET* 1.3 67.3 + - - +
131A LYS 3.1 1.3 - - - -
132A ALA* 3.5 4.5 - - + +
133A ALA* 3.0 22.9 + - - +
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Residues in contact with MET 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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45A LEU* 3.4 24.1 - - + +
80A TRP* 3.1 38.3 - - + +
126A VAL* 3.3 24.4 + - - +
127A LYS* 3.4 6.1 + - - +
129A PHE* 1.3 78.1 - - - +
131A LYS* 1.3 63.9 + - - +
133A ALA* 3.2 3.8 + - - +
134A LYS* 3.2 24.1 + - - +
149A GLU* 4.3 8.7 - - + +
151A TYR* 3.3 41.7 - - + -
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Residues in contact with LYS 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 LYS 3.3 13.6 + - - +
128A TYR* 3.8 20.9 - - + +
130A MET* 1.3 81.9 - - - +
132A ALA* 1.3 63.0 + - - +
133A ALA 3.1 1.2 + - - -
134A LYS* 3.7 4.2 + - - +
135A GLU* 3.1 62.8 + - - +
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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
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47A GLY 5.6 0.2 - - - +
48A HIS* 3.4 36.2 - - + +
49A LEU* 5.4 1.5 - - - +
128A TYR* 3.0 27.8 + - + +
129A PHE* 3.7 10.8 - - + +
130A MET 3.3 0.2 - - - -
131A LYS* 1.3 79.5 - - - +
133A ALA* 1.3 52.0 + - - +
135A GLU* 4.3 4.6 - - - +
136A THR* 2.4 32.3 + - - -
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Residues in contact with ALA 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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43A PRO* 5.3 0.9 - - + -
45A LEU* 4.4 5.8 - - + -
49A LEU* 4.4 22.0 - - + -
80A TRP* 3.9 24.5 - - + -
129A PHE 3.0 15.8 + - - +
130A MET 3.5 5.2 - - - +
131A LYS 3.0 0.2 - - - -
132A ALA* 1.3 74.7 - - - +
134A LYS* 1.3 58.8 + - - +
135A GLU 2.9 3.6 - - - -
136A THR* 2.6 27.5 + - - -
137A PHE* 2.8 17.5 + - + -
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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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80A TRP* 3.6 18.9 - - + +
130A MET 3.2 10.7 + - - +
131A LYS* 4.2 5.2 - - - +
133A ALA* 1.3 78.3 - - - +
135A GLU* 1.3 60.3 + - + +
137A PHE* 4.0 0.7 - - - -
138A ILE* 3.1 28.3 + - + +
146A TRP* 3.6 34.3 - - + -
149A GLU* 3.3 38.1 + - - +
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Residues in contact with GLU 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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131A LYS* 3.1 52.3 + - - +
132A ALA* 4.5 4.4 - - - +
133A ALA 2.7 5.1 + - - -
134A LYS* 1.3 78.9 + - + +
136A THR* 1.3 54.8 + - - +
138A ILE* 3.0 12.2 - - + +
139A ARG* 2.5 43.4 + - + +
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Residues in contact with THR 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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48A HIS* 5.2 0.7 - - - -
49A LEU* 5.6 5.2 - - + +
132A ALA 2.4 24.4 + - - -
133A ALA* 2.6 13.0 + - - -
135A GLU* 1.3 72.4 - - - +
137A PHE* 1.3 66.6 + - - +
139A ARG* 3.6 6.3 - - - -
140A ALA* 3.1 22.9 + - - +
661A PHE* 3.9 20.9 - - + -
662A ILE* 3.2 55.9 - - + +
665A ILE* 4.3 2.5 - - + -
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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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43A PRO* 4.4 2.7 - - + -
49A LEU* 3.4 36.3 - - + -
57A TYR* 3.7 26.7 - + - -
78A MET* 3.3 48.7 - - + -
80A TRP* 3.8 17.7 - + - -
133A ALA* 2.8 22.0 + - + +
136A THR* 1.3 75.6 - - - +
138A ILE* 1.3 62.1 + - - +
140A ALA* 3.1 13.2 + - - +
141A GLY 3.2 7.8 + - - -
142A PHE* 3.5 37.5 + + + -
144A VAL* 5.2 2.0 - - + -
146A TRP* 3.9 18.6 - + + -
661A PHE* 4.7 7.9 - + - -
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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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14A GLN* 3.4 25.6 + - + +
17A TRP* 6.1 2.2 - - + -
18A LEU* 3.9 31.9 - - + -
134A LYS* 3.1 17.1 + - + +
135A GLU* 3.0 24.7 - - + +
137A PHE* 1.3 76.2 - - - +
139A ARG* 1.3 58.7 + - + +
140A ALA 3.1 5.6 - - - -
141A GLY* 3.1 15.8 + - - -
142A PHE 4.5 17.5 - - - +
146A TRP* 3.8 27.8 - - + +
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Residues in contact with ARG 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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7A LYS* 5.5 6.8 - - - +
10A GLU* 3.8 15.0 + - - +
11A GLU* 6.0 3.1 - - - -
14A GLN* 3.4 30.6 + - - +
135A GLU* 2.5 26.4 + - + +
136A THR* 3.6 10.5 - - - +
137A PHE 3.2 0.2 - - - -
138A ILE* 1.3 74.7 - - + +
140A ALA* 1.3 56.6 + - - +
141A GLY 3.4 1.1 - - - -
662A ILE* 3.8 27.7 - - + +
665A ILE* 3.4 21.2 - - + +
666A GLU* 2.3 48.7 + - - +
670A ALA* 3.9 1.6 - - - +
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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
------------------------------------------------------------
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