Contacts of the helix formed by residues 129 - 140 (chain J) in PDB entry 5ANC
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 THR 129 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120J VAL 2.7 25.8 + - - -
121J ASN* 3.2 7.3 + - - -
122J PRO* 3.6 25.6 - - + -
126J ARG* 3.8 15.3 - - + +
128J TYR* 1.3 83.8 + - - +
130J VAL* 1.3 63.1 + - - +
131J ILE* 3.3 7.6 - - - +
132J LEU* 3.3 22.5 + - + +
133J ILE* 3.3 20.8 + - - +
623K GLU* 4.0 16.6 - - + +
1096K LYS* 4.7 13.1 - - + +
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Residues in contact with VAL 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ALA* 4.1 6.0 - - + +
113J THR* 5.9 0.9 - - - -
116J ALA* 3.5 32.1 - - + +
128J TYR* 4.2 17.9 - - + +
129J THR* 1.3 73.4 - - - +
131J ILE* 1.3 69.0 + - + +
133J ILE* 3.2 13.3 + - + +
134J GLU* 3.1 27.7 + - + +
1092K ASN 6.0 0.4 - - - +
1096K LYS* 4.8 14.0 - - - +
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Residues in contact with ILE 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J THR* 4.8 4.9 - - - -
130J VAL* 1.3 84.0 - - + +
132J LEU* 1.3 83.2 + - + +
134J GLU* 3.2 19.0 + - + +
135J ARG* 2.9 28.0 + - + +
623K GLU* 5.1 8.7 - - + -
684K SER* 4.2 20.0 - - - +
1093K ALA* 6.1 4.7 - - + -
1096K LYS* 5.6 9.4 - - - +
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 4.4 9.0 - - + +
122J PRO* 4.2 3.6 - - + -
129J THR* 3.3 30.5 + - + +
130J VAL 3.2 0.6 - - - -
131J ILE* 1.3 89.5 - - + +
133J ILE* 1.3 60.4 + - - +
135J ARG* 3.6 25.5 + - + +
136J ALA* 3.1 27.2 + - - +
623K GLU* 3.8 32.8 - - + +
624K PRO* 3.3 27.1 - - + +
630K MET* 3.7 26.7 - - + -
684K SER* 5.9 2.7 - - - -
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Residues in contact with ILE 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ALA* 3.6 24.9 - - + +
115J VAL* 3.5 31.6 - - + +
116J ALA* 3.6 12.1 - - - +
119J CYS* 3.4 29.4 - - + -
120J VAL* 3.8 23.3 - - + +
129J THR 3.5 6.7 - - - +
130J VAL* 3.2 21.5 + - - +
132J LEU* 1.3 75.6 - - - +
134J GLU* 1.3 64.2 + - - +
136J ALA* 3.2 5.8 + - - +
137J MET* 3.1 41.6 + - + +
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Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J PHE* 3.1 46.0 - - + +
109J ARG* 3.6 29.5 - - - +
112J ALA* 3.3 25.1 - - + -
130J VAL* 3.1 9.6 + - - +
131J ILE* 3.3 21.8 - - + +
133J ILE* 1.3 79.5 - - - +
135J ARG* 1.3 63.9 + - - +
137J MET* 3.2 11.1 + - - +
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Residues in contact with ARG 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 6.0 1.4 - - - +
131J ILE* 2.9 18.0 + - + +
132J LEU* 3.6 30.0 + - + +
134J GLU* 1.3 77.7 - - - +
136J ALA* 1.3 69.6 + - - +
137J MET 3.4 0.5 + - - -
138J LYS* 3.6 4.0 + - - +
139J ASP* 2.8 43.4 + - - +
164J LYS* 5.8 0.4 - - - +
624K PRO 3.5 16.9 + - - -
625K LYS* 3.6 16.2 - - + +
626K HIS* 3.2 32.2 + - + +
627K PRO* 3.3 34.4 - - - +
630K MET* 4.0 18.3 - - - +
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 5.5 8.3 - - + -
132J LEU 3.1 15.3 + - - +
133J ILE* 3.2 8.3 + - - +
135J ARG* 1.3 88.8 - - - +
137J MET* 1.3 72.5 - - + +
138J LYS 3.3 0.2 - - - -
139J ASP* 3.3 17.6 + - - -
140J ILE* 3.4 12.3 + - - +
161J LEU* 5.6 0.2 - - + -
164J LYS* 3.5 30.6 + - - +
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Residues in contact with MET 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J PHE* 3.3 26.9 - - + +
111J ILE* 3.5 45.1 - - + +
112J ALA* 4.9 0.4 - - + -
115J VAL* 5.2 2.5 - - + -
120J VAL* 6.1 1.8 - - + -
133J ILE* 3.1 41.7 + - + +
134J GLU* 3.2 12.0 + - - +
136J ALA* 1.3 84.6 - - + +
138J LYS* 1.3 58.4 + - - +
140J ILE* 3.1 23.8 - - + +
142J TYR* 3.3 16.2 + - + +
144J VAL* 5.2 0.9 - - + -
157J VAL* 4.2 26.2 - - + +
161J LEU* 6.0 7.9 - - + -
164J LYS* 6.1 1.1 - - - -
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Residues in contact with LYS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J PHE* 3.5 36.3 - - + -
134J GLU 4.1 0.6 + - - -
135J ARG 3.6 5.5 + - - +
136J ALA 3.3 0.2 - - - -
137J MET* 1.3 75.2 - - - +
139J ASP* 1.3 66.1 + - - +
140J ILE 3.3 1.8 - - - -
141J HIS* 3.3 22.8 + - - +
142J TYR 3.3 20.6 + - - +
144J VAL* 3.2 25.7 - - + +
2555N U 5.1 1.2 + - - -
2556N C 3.6 29.8 + - - +
2557N A 4.7 3.9 + - - +
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Residues in contact with ASP 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ARG* 2.8 46.9 + - - +
136J ALA* 3.3 10.6 + - - +
138J LYS* 1.3 80.1 - - - +
140J ILE* 1.3 58.1 + - - +
141J HIS* 3.4 13.4 + - - -
164J LYS* 4.8 6.1 - - - +
626K HIS* 3.4 40.5 + - + -
627K PRO* 4.8 5.6 - - + +
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Residues in contact with ILE 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA 3.4 10.4 + - - +
137J MET* 3.1 24.0 - - + +
139J ASP* 1.3 76.1 - - - +
141J HIS* 1.3 76.2 + - - +
142J TYR* 4.2 6.1 - - + -
157J VAL* 6.5 0.7 - - + -
160J GLN* 3.5 45.9 + - + +
163J GLU* 4.9 15.9 - - + +
164J LYS* 4.2 17.9 - - - +
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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