Contacts of the helix formed by residues 129 - 142 (chain A) in PDB entry 1A76
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 PRO 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 5.0 13.5 - - + +
124A VAL* 3.5 24.2 - - + -
128A THR* 1.3 88.2 - - - +
130A LYS* 1.3 50.2 + - - +
132A VAL* 3.2 6.4 + - + -
133A GLU* 2.4 50.8 + - - +
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Residues in contact with LYS 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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58A TYR* 5.7 0.2 - - - +
128A THR* 3.1 7.4 - - - +
129A PRO* 1.3 81.5 - - - +
131A MET* 1.3 58.6 + - - +
133A GLU* 3.3 8.0 + - + +
134A ASN* 2.9 54.8 + - - +
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Residues in contact with MET 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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36A LEU* 4.5 8.3 - - - -
54A ILE* 3.7 41.7 - - + +
57A ALA* 4.0 22.0 - - + -
58A TYR* 3.6 28.7 - - + +
126A TYR 3.1 26.7 - - - +
127A LEU* 4.1 15.5 - - + -
128A THR* 3.0 20.4 + - + +
130A LYS* 1.3 76.4 - - - +
132A VAL* 1.3 61.6 + - - +
134A ASN* 3.2 3.2 + - - +
135A CYS* 3.0 28.7 + - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.6 35.0 - - + -
32A LEU* 4.9 0.7 - - - -
79A PHE* 4.2 8.1 - - + -
82A GLU* 4.1 22.2 - - + +
127A LEU* 3.4 25.8 - - + +
128A THR 2.9 21.4 + - - +
129A PRO* 3.4 9.9 - - + +
131A MET* 1.3 74.3 - - - +
133A GLU* 1.3 74.7 + - - +
135A CYS* 3.2 9.1 + - - +
136A LYS* 3.2 22.7 + - - +
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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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82A GLU* 2.7 23.3 - - - +
83A PRO* 6.1 0.4 - - - -
129A PRO* 2.4 37.6 + - - +
130A LYS* 3.6 12.1 - - + +
131A MET 3.3 0.2 - - - -
132A VAL* 1.3 79.0 - - - +
134A ASN* 1.3 56.6 + - - +
136A LYS* 3.1 39.2 + - + +
137A TYR* 3.0 27.3 + - - +
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Residues in contact with ASN 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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58A TYR* 3.1 31.8 + - + +
130A LYS* 2.9 48.0 + - - +
131A MET 3.4 9.2 - - - +
133A GLU* 1.3 76.9 - - - +
135A CYS* 1.3 60.2 + - - +
137A TYR* 3.4 10.5 + - - +
138A LEU* 3.0 28.4 + - - +
289A PHE* 4.0 23.7 - - + -
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Residues in contact with CYS 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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32A LEU* 4.1 19.1 - - + -
57A ALA* 3.8 21.3 - - - -
58A TYR* 3.7 20.9 - - - -
61A VAL* 3.9 21.3 - - + +
79A PHE* 4.8 6.1 - - + -
131A MET* 3.0 18.2 + - - -
132A VAL* 3.2 10.7 + - - +
134A ASN* 1.3 73.8 - - - +
136A LYS* 1.3 64.8 + - - +
138A LEU* 3.3 7.8 + - - +
139A LEU* 3.0 29.4 + - - +
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Residues in contact with LYS 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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79A PHE* 3.6 45.4 - - + +
81A GLY* 4.7 2.8 - - - -
82A GLU* 2.8 27.3 + - - -
83A PRO* 5.5 0.8 - - - +
132A VAL* 3.2 11.2 + - - +
133A GLU* 3.1 30.2 + - - +
135A CYS* 1.3 76.7 - - - +
137A TYR* 1.3 61.7 + - - +
139A LEU* 3.2 7.1 + - - +
140A SER* 3.0 19.1 + - - -
146A TYR* 3.4 34.9 - - + +
148A GLU* 2.9 32.6 + - - +
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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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133A GLU 3.0 13.0 + - - +
134A ASN* 3.5 13.2 - - - +
135A CYS 3.2 0.2 - - - -
136A LYS* 1.3 77.6 - - - +
138A LEU* 1.3 62.6 + - - +
140A SER* 2.5 30.5 + - - -
141A LEU* 2.9 45.1 + - + +
285A GLY* 5.1 3.8 + - - -
288A LYS* 6.1 1.2 - - - +
289A PHE* 4.0 32.8 - + + -
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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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58A TYR* 3.5 41.3 - - + +
61A VAL* 3.8 17.9 - - + -
62A PHE* 4.3 5.2 - - + +
134A ASN 3.0 17.7 + - - +
135A CYS* 3.5 5.4 - - - +
137A TYR* 1.3 79.1 - - - +
139A LEU* 1.3 57.2 + - - +
141A LEU* 3.2 11.4 + - + +
142A MET* 2.9 51.0 + - + +
286A ILE* 4.7 10.8 - - + -
289A PHE* 4.0 21.1 - - + -
290A LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 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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61A VAL* 3.6 24.0 - - + -
65A THR* 4.3 3.4 - - - +
77A TRP* 3.5 48.2 - - + +
79A PHE* 3.6 29.6 - - + -
135A CYS 3.0 15.9 + - - +
136A LYS* 3.5 7.9 - - - +
137A TYR 3.2 0.2 - - - -
138A LEU* 1.3 76.2 - - - +
140A SER* 1.3 61.3 + - - +
142A MET* 3.1 6.3 + - - -
143A GLY 3.0 4.2 + - - -
144A ILE* 2.9 53.4 + - + +
146A TYR* 4.3 7.4 - - + -
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Residues in contact with SER 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 LYS 3.0 11.9 + - - -
137A TYR* 2.5 34.0 + - - -
139A LEU* 1.3 79.3 - - - +
141A LEU* 1.3 64.0 + - - +
143A GLY* 3.1 14.2 + - - +
144A ILE 4.3 4.0 + - - +
146A TYR* 4.7 10.9 - - - -
279A LYS* 6.1 0.2 - - - +
280A LEU 5.6 0.2 - - - +
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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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137A TYR* 2.9 58.0 + - + +
138A LEU* 3.2 12.8 + - + +
140A SER* 1.3 83.5 + - - +
142A MET* 1.3 59.5 + - - +
143A GLY 3.2 1.1 + - - -
280A LEU 4.6 0.3 - - - +
281A PRO* 3.4 1.0 - - - +
282A ASP* 2.9 56.5 + - + +
285A GLY* 3.7 26.0 - - - +
286A ILE* 3.6 17.6 - - + +
289A PHE* 4.3 7.0 - - + -
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Residues in contact with MET 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.3 8.5 - - - +
62A PHE* 3.7 51.4 - - + +
65A THR* 3.9 26.0 - - + -
66A ILE* 4.3 3.1 - - + -
138A LEU* 2.9 34.1 + - + +
139A LEU* 3.1 9.2 + - - +
141A LEU* 1.3 77.1 - - - +
143A GLY* 1.3 58.2 + - - +
144A ILE* 3.1 11.3 + - + +
281A PRO* 3.7 5.9 - - - +
286A ILE* 3.9 20.6 - - + -
308A LEU* 3.6 27.9 - - + +
312A ILE* 3.6 12.5 - - - +
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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