Contacts of the helix formed by residues 134 - 153 (chain A) in PDB entry 5OND
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LYS* 4.8 2.7 - - - +
132A GLU* 2.9 20.1 + - - +
133A PRO* 1.3 77.7 - - + +
135A GLY* 1.3 66.8 + - - +
136A GLU* 3.1 15.4 + - - +
137A ALA* 2.6 33.4 + - + +
138A ARG* 3.0 19.7 + - - +
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Residues in contact with GLY 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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48A GLU* 4.1 3.8 + - - -
52A PRO* 3.6 22.4 - - - +
133A PRO 3.9 1.0 + - - -
134A ASP* 1.3 75.7 + - - +
136A GLU* 1.3 57.8 + - - +
138A ARG* 2.9 45.1 + - - +
139A SER* 2.9 17.0 + - - -
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 5.1 6.7 + - - -
52A PRO* 3.8 28.2 - - + +
53A ASN* 4.5 6.6 + - - -
54A TYR* 5.7 2.4 - - - -
134A ASP* 3.1 12.7 + - - +
135A GLY* 1.3 75.2 - - - +
137A ALA* 1.3 63.2 + - - +
139A SER* 3.3 9.9 + - - -
140A MET* 3.0 22.9 + - - +
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Residues in contact with ALA 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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132A GLU* 3.6 32.1 - - + +
134A ASP* 2.6 21.1 + - + +
135A GLY 3.2 0.2 - - - -
136A GLU* 1.3 74.4 - - - +
138A ARG* 1.4 57.3 + - - +
140A MET* 3.3 12.5 + - + +
141A LEU* 2.8 34.1 + - + +
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Residues in contact with ARG 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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33A ILE* 3.9 11.3 - - - +
35A LEU* 3.6 12.3 - - - +
48A GLU* 2.7 26.5 + - - +
49A PRO 3.0 22.6 + - - -
50A LEU* 2.7 40.3 + - - +
51A PHE* 3.7 11.4 - - + -
129A ILE* 3.2 23.7 - - + +
132A GLU* 2.8 49.2 + - + +
133A PRO 3.1 22.0 + - - -
134A ASP 3.0 7.6 + - - +
135A GLY* 2.9 21.9 + - - +
137A ALA* 1.4 74.8 - - - +
139A SER* 1.3 57.3 + - - +
141A LEU* 3.1 10.1 + - - +
142A LEU* 2.8 26.3 + - - +
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Residues in contact with SER 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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51A PHE* 3.3 38.7 - - - +
52A PRO* 3.7 3.5 + - - +
54A TYR* 3.6 27.1 - - - -
135A GLY 2.9 8.0 + - - -
136A GLU* 3.7 13.9 + - - -
138A ARG* 1.3 73.4 - - - +
140A MET* 1.3 67.7 + - - +
142A LEU* 2.8 5.2 + - - +
143A LEU* 2.8 28.5 + - - +
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Residues in contact with MET 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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136A GLU 3.0 13.9 + - - +
137A ALA* 3.6 14.4 - - + +
139A SER* 1.3 75.7 - - - +
141A LEU* 1.3 90.6 + - + +
143A LEU* 3.3 9.5 + - + +
144A ASN* 3.1 45.5 + - - +
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Residues in contact with LEU 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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125A GLY 5.2 1.3 - - - +
128A ALA* 4.2 13.0 - - + +
129A ILE* 3.5 37.7 - - + +
132A GLU* 4.1 21.5 - - + +
137A ALA* 2.8 20.5 + - + +
138A ARG* 3.1 7.6 + - - +
140A MET* 1.3 94.1 - - + +
142A LEU* 1.3 62.8 + - - +
144A ASN* 3.3 9.7 + - + +
145A LEU* 3.0 24.1 + - - +
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Residues in contact with LEU 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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6A LEU* 3.6 25.6 - - + -
51A PHE* 3.7 49.8 - - + -
54A TYR* 5.2 2.2 - - + -
56A PHE* 3.8 15.7 - - + -
92A VAL* 4.6 3.4 - - + -
126A PHE* 4.4 15.3 - - + -
129A ILE* 3.9 6.5 - - + -
138A ARG 2.8 13.1 + - - +
139A SER* 2.8 10.6 + - - +
141A LEU* 1.3 77.9 - - - +
143A LEU* 1.3 67.1 + - + +
145A LEU* 3.0 6.2 + - + +
146A ILE* 2.9 45.8 + - + +
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Residues in contact with LEU 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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6A LEU* 3.9 26.7 - - + -
54A TYR* 3.7 24.5 - - + +
79A VAL* 4.0 24.5 - - + -
139A SER 2.8 23.4 + - - +
140A MET* 3.8 9.6 - - + +
142A LEU* 1.3 75.4 - - + +
144A ASN* 1.3 66.9 + - - +
146A ILE* 3.2 6.5 + - + +
147A ASN* 3.0 23.7 + - - +
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Residues in contact with ASN 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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140A MET* 3.1 42.5 + - - +
141A LEU* 3.7 11.0 - - + +
143A LEU* 1.3 78.6 - - - +
145A LEU* 1.3 59.5 + - - +
147A ASN* 3.4 6.3 + - - +
148A LYS* 2.9 29.8 + - - +
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Residues in contact with LEU 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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92A VAL* 4.8 4.9 - - + -
121A GLY* 3.7 9.4 - - - +
122A ALA* 3.7 17.0 - - + +
125A GLY* 3.8 24.0 - - - -
126A PHE* 3.6 38.4 - - + -
129A ILE* 4.2 9.4 - - + -
141A LEU 3.0 15.4 + - - +
142A LEU* 3.5 5.6 - - + +
144A ASN* 1.3 78.6 - - - +
146A ILE* 1.3 59.1 + - + +
148A LYS* 3.5 9.7 + - + +
149A GLU* 2.9 46.7 + - + +
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Residues in contact with ILE 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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6A LEU* 3.7 21.3 - - + -
56A PHE* 4.6 1.1 - - + -
79A VAL* 5.4 5.4 - - + -
86A ALA* 4.2 14.1 - - + -
88A VAL* 4.3 32.1 - - + -
89A PRO* 4.9 2.9 - - + -
92A VAL* 4.4 9.4 - - + -
142A LEU* 2.9 47.2 + - + +
143A LEU* 3.8 5.8 - - + +
145A LEU* 1.3 74.8 - - - +
147A ASN* 1.3 66.8 + - - +
149A GLU* 3.3 4.1 + - - +
150A ILE* 2.9 51.8 + - + +
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Residues in contact with ASN 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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80A ARG 5.1 5.9 + - - -
81A PHE* 3.4 29.4 - - - +
143A LEU 3.0 12.6 + - - +
144A ASN* 3.5 11.7 - - - +
146A ILE* 1.3 78.7 - - - +
148A LYS* 1.3 63.5 + - - +
150A ILE* 3.7 1.4 - - - +
151A LYS* 3.0 51.0 + - - +
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Residues in contact with LYS 148 (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 GLY* 3.8 31.8 + - - -
144A ASN 2.9 18.9 + - - +
145A LEU* 3.8 9.4 - - + +
147A ASN* 1.3 77.2 + - - +
149A GLU* 1.3 65.3 + - - +
151A LYS* 3.4 7.7 + - - +
152A HIS* 2.9 30.4 + - + +
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Residues in contact with GLU 149 (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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89A PRO* 4.0 22.2 - - + +
91A ALA* 5.3 1.7 - - - +
92A VAL* 4.3 10.3 - - + -
119A THR* 3.1 38.2 + - - +
121A GLY* 3.5 7.8 - - - -
122A ALA* 3.0 23.8 + - + +
145A LEU* 2.9 36.5 + - + +
146A ILE 3.9 3.1 - - - +
148A LYS* 1.3 80.2 - - + +
150A ILE* 1.3 61.4 + - - +
152A HIS* 3.4 12.4 + - - +
153A SER* 3.3 18.4 + - - -
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Residues in contact with ILE 150 (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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81A PHE* 3.8 39.0 - - + -
86A ALA* 3.8 15.9 - - + -
87A ILE 3.4 27.8 - - - +
89A PRO* 4.0 11.0 - - + -
146A ILE* 2.9 37.5 + - + +
147A ASN 3.7 3.1 - - - +
149A GLU* 1.3 73.9 - - - +
151A LYS* 1.3 67.9 + - - +
153A SER* 2.8 28.1 + - - +
154A VAL* 3.5 7.5 + - + +
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Residues in contact with LYS 151 (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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81A PHE* 3.5 24.5 - - + -
147A ASN* 3.0 43.5 + - - +
148A LYS* 3.7 7.4 - - - +
150A ILE* 1.3 74.2 - - - +
152A HIS* 1.3 62.9 + - - +
154A VAL* 3.0 29.3 + - - +
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Residues in contact with HIS 152 (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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119A THR* 5.8 9.7 - - + +
148A LYS* 2.9 20.1 + - + +
149A GLU* 3.5 17.0 + - - +
150A ILE 3.1 0.4 - - - -
151A LYS* 1.3 75.3 - - - +
153A SER* 1.3 58.7 + - - +
154A VAL 3.2 6.4 + - - +
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 6.5 0.7 - - - -
149A GLU 3.3 10.0 + - - -
150A ILE* 2.8 22.8 + - - +
152A HIS* 1.3 75.8 - - - +
154A VAL* 1.3 63.4 + - - +
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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