Contacts of the helix formed by residues 121 - 141 (chain A) in PDB entry 1O0W
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 ARG 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLU* 2.7 31.8 + - - -
116A THR* 3.4 20.6 + - - -
117A GLY 3.5 3.9 + - - +
118A GLY* 3.1 34.9 + - - +
119A ARG 3.5 0.2 - - - -
120A ASP* 1.3 75.1 - - - +
122A ASP* 1.3 68.5 + - - +
123A SER* 3.4 23.6 - - - +
124A ILE* 3.0 15.9 + - + +
125A LEU* 2.9 24.2 + - - +
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Residues in contact with ASP 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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91A GLU* 3.7 19.2 - - + +
92A GLU* 5.0 10.0 - - - +
95A ALA* 3.9 16.9 - - + +
99A ARG* 2.7 43.1 + - - +
120A ASP 3.4 1.1 + - - +
121A ARG* 1.3 73.4 - - - +
123A SER* 1.3 58.2 + - - +
125A LEU* 3.2 2.6 + - - +
126A ALA* 2.9 32.4 + - - +
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Residues in contact with SER 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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91A GLU* 3.5 24.3 - - - -
121A ARG* 3.4 22.6 - - - +
122A ASP* 1.3 79.0 - - - +
124A ILE* 1.3 61.7 + - - +
126A ALA* 3.9 0.4 - - - +
127A ASP* 2.9 41.8 + - - +
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Residues in contact with ILE 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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32A HIS* 3.5 41.3 - - + +
50A ASN* 5.4 0.5 + - - -
107A LEU* 3.6 27.6 - - + -
109A LEU* 4.4 5.6 - - + -
113A GLU* 3.7 25.4 - - + +
118A GLY* 3.6 24.7 - - - +
121A ARG* 3.0 24.2 + - + +
123A SER* 1.3 84.4 + - - +
125A LEU* 1.3 58.6 + - - +
127A ASP* 3.7 7.4 - - - +
128A ALA* 2.9 28.5 + - + +
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Residues in contact with LEU 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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95A ALA* 4.5 4.7 - - + -
98A SER* 3.2 28.1 + - - -
99A ARG* 3.5 49.4 - - + +
103A LEU* 3.9 4.0 - - + +
104A GLY* 3.8 34.3 - - - +
107A LEU* 4.1 9.6 - - + -
119A ARG 3.8 11.0 - - - +
120A ASP* 4.1 7.2 - - - -
121A ARG 2.9 19.0 + - - +
122A ASP* 3.7 4.0 - - - +
124A ILE* 1.3 77.5 - - + +
126A ALA* 1.3 63.5 + - - +
128A ALA* 3.2 5.8 + - - +
129A PHE 2.9 18.0 + - - -
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Residues in contact with ALA 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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91A GLU* 3.8 25.8 - - + +
94A LEU* 3.9 29.0 - - + +
95A ALA* 4.4 2.0 - - - +
98A SER* 4.4 2.7 - - - -
122A ASP 2.9 17.9 + - - +
123A SER* 3.9 2.9 - - - +
125A LEU* 1.3 75.7 - - - +
127A ASP* 1.3 65.6 + - - +
129A PHE* 3.1 4.9 + - - +
130A GLU* 3.0 27.7 + - - +
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Residues in contact with ASP 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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32A HIS* 6.0 3.1 - - + -
50A ASN* 4.6 8.1 - - - +
54A GLU* 3.3 42.1 - - - +
123A SER* 2.9 30.2 + - - +
124A ILE* 3.7 8.1 - - - +
126A ALA* 1.3 79.7 - - - +
128A ALA* 1.3 63.4 + - - +
130A GLU* 3.2 8.3 + - - +
131A ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 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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29A ALA* 4.0 12.1 - - - +
30A LEU* 5.2 0.7 - - + -
50A ASN* 3.8 15.4 - - - +
103A LEU* 4.0 8.5 - - + +
107A LEU* 3.4 31.0 - - + -
124A ILE* 2.9 19.9 + - + +
125A LEU 3.7 3.8 - - - +
127A ASP* 1.3 76.0 - - - +
129A PHE* 1.3 58.5 + - - +
131A ALA* 3.3 2.5 + - - +
132A LEU* 2.8 29.1 + - - +
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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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94A LEU* 4.0 30.1 - - + +
97A VAL* 3.6 20.9 - - + -
98A SER* 3.4 24.7 - - - +
101A MET* 3.4 36.3 - - + -
103A LEU* 3.9 6.9 - - + +
125A LEU 2.9 6.5 + - - -
126A ALA* 3.1 10.0 + - - +
128A ALA* 1.3 78.7 - - - +
130A GLU* 1.3 64.4 + - - +
132A LEU* 3.1 10.2 + - + +
133A LEU* 3.0 50.7 + - + +
149A PHE* 3.9 22.7 - + - -
153A PHE* 4.3 11.2 - + - -
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Residues in contact with GLU 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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54A GLU* 3.6 33.6 - - + +
57A GLY* 3.1 23.3 - - - -
58A ASP* 2.5 42.6 - - - +
61A LEU* 3.6 19.2 - - + +
89A ALA 4.9 1.7 - - - +
94A LEU* 3.6 20.0 - - + +
126A ALA* 3.0 16.3 + - - +
127A ASP* 3.6 10.4 - - - +
129A PHE* 1.3 77.4 - - + +
131A ALA* 1.3 62.1 + - - +
133A LEU* 3.2 11.6 + - - +
134A ALA 3.1 7.8 + - - -
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Residues in contact with ALA 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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29A ALA* 3.7 11.3 - - - +
50A ASN* 3.6 31.0 - - + +
53A LEU* 3.8 13.9 - - + +
54A GLU* 3.7 17.2 - - - +
127A ASP 3.0 13.4 + - - +
128A ALA 3.5 7.2 - - - +
130A GLU* 1.3 76.0 - - - +
132A LEU* 1.3 57.9 + - - +
134A ALA* 3.1 4.5 + - - +
135A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 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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12A PHE* 3.8 36.6 - - + -
18A ILE* 4.8 2.9 - - + -
20A PHE* 3.9 23.8 - - + -
26A LEU* 4.0 8.7 - - + -
29A ALA* 3.8 10.9 - - + +
30A LEU* 6.0 2.0 - - + -
101A MET* 4.0 24.9 - - + -
103A LEU* 5.0 7.2 - - + -
128A ALA 2.8 14.2 + - - +
129A PHE* 3.3 17.9 - - + +
131A ALA* 1.3 76.9 - - - +
133A LEU* 1.3 56.6 - - + +
135A ALA* 3.1 3.9 + - + +
136A ILE* 2.8 43.7 + - + +
149A PHE* 5.2 1.8 - - + -
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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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57A GLY 4.5 2.0 - - - +
60A VAL* 4.4 11.4 - - + -
61A LEU* 3.9 36.8 - - + -
64A PHE* 6.0 2.5 - - + -
129A PHE* 3.0 44.7 + - + +
130A GLU* 3.2 11.2 + - - +
132A LEU* 1.3 77.7 - - + +
134A ALA* 1.3 57.0 + - - +
136A ILE* 3.4 3.8 + - - +
137A TYR* 2.8 30.6 + - - +
145A ILE* 3.6 19.6 - - + +
149A PHE* 3.5 37.7 - - + -
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Residues in contact with ALA 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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53A LEU* 3.0 40.8 - - + +
56A LEU* 3.9 12.6 - - + -
57A GLY* 3.5 13.8 - - - +
60A VAL* 4.5 3.1 - - - -
130A GLU 3.1 6.3 + - - -
131A ALA 3.1 5.1 + - - +
133A LEU* 1.3 77.2 - - - +
135A ALA* 1.3 56.8 + - - +
137A TYR* 3.4 6.9 - - - +
138A LEU* 2.8 36.3 + - - +
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Residues in contact with ALA 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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20A PHE* 3.6 20.0 - - + -
25A LEU* 3.6 32.5 - - + +
29A ALA* 4.1 7.6 - - + -
53A LEU* 4.1 10.0 - - + +
131A ALA 2.9 12.9 + - - +
132A LEU* 3.1 7.6 + - - +
134A ALA* 1.3 75.8 - - - +
136A ILE* 1.3 58.2 + - - +
138A LEU* 3.4 2.9 + - - +
139A ASP* 2.8 32.9 + - - +
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Residues in contact with ILE 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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18A ILE* 3.9 15.0 - - + -
20A PHE* 3.6 24.0 - - + -
132A LEU* 2.8 36.2 + - + +
133A LEU* 3.8 3.8 - - - +
135A ALA* 1.3 71.9 - - - +
137A TYR* 1.3 60.3 + - - +
139A ASP* 4.4 1.8 - - - +
140A GLN* 2.7 35.1 + - + +
141A GLY 3.2 4.5 + - - -
144A LYS* 3.6 30.5 - - + -
145A ILE* 3.9 16.4 - - + -
148A LEU* 3.9 20.2 - - + -
149A PHE* 4.0 16.6 - - + -
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Residues in contact with TYR 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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56A LEU* 4.4 6.7 - - + -
60A VAL* 3.9 18.6 - - + -
133A LEU 2.8 18.5 + - - +
134A ALA 3.4 4.3 - - - +
136A ILE* 1.3 76.9 - - - +
138A LEU* 1.3 73.0 + - + +
141A GLY* 2.8 28.8 + - - +
142A TYR* 3.6 40.2 - + + -
145A ILE* 3.6 15.9 - - + +
63B LEU* 3.8 25.4 - - + +
67B GLU* 2.7 41.1 + - + -
142B TYR* 3.3 22.0 - + - -
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Residues in contact with LEU 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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25A LEU* 4.1 19.9 - - + +
53A LEU* 3.6 16.4 - - + -
56A LEU* 3.8 20.4 - - + -
134A ALA 2.8 18.8 + - - +
135A ALA 3.8 3.1 - - - +
137A TYR* 1.3 84.0 - - + +
139A ASP* 1.3 60.7 + - - +
141A GLY 4.9 0.3 + - - -
70B TYR* 3.3 39.7 - - + +
71B LYS* 3.9 29.4 - - - +
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Residues in contact with ASP 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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20A PHE* 3.4 15.3 - - + -
21A LYS* 2.7 60.4 + - - +
22A ASN* 2.8 33.3 + - - +
25A LEU* 3.7 9.6 - - + +
135A ALA 2.8 21.5 + - - +
136A ILE 4.0 1.1 - - - +
138A LEU* 1.3 76.9 - - - +
140A GLN* 1.3 79.5 + - - +
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Residues in contact with GLN 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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18A ILE* 5.1 3.9 - - - +
19A ASN 2.9 26.7 + - - +
20A PHE* 3.8 10.5 - - - +
21A LYS* 4.4 17.3 - - + +
136A ILE* 2.7 19.1 + - - +
139A ASP* 1.3 101.8 + - - +
141A GLY* 1.3 59.5 + - - +
143A GLU* 5.7 0.9 - - - +
144A LYS* 3.4 49.2 + - + +
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Residues in contact with GLY 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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136A ILE 3.2 2.7 + - - +
137A TYR* 2.8 26.0 + - - -
138A LEU 4.9 0.2 + - - -
139A ASP 3.9 0.2 - - - -
140A GLN* 1.3 77.2 - - - +
142A TYR* 1.3 65.7 + - - -
143A GLU 3.3 2.9 - - - -
144A LYS* 3.2 17.5 + - - +
145A ILE* 3.5 9.4 + - - +
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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