Contacts of the helix formed by residues 140 - 148 (chain A) in PDB entry 1J71
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 ASN 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER* 3.2 34.4 + - - +
37A ASP* 5.5 0.4 - - - -
38A LEU* 5.9 1.8 - - + +
109A GLN* 3.6 6.7 - - - +
125A GLY 4.0 6.0 + - - +
127A GLY 3.0 27.3 + - - +
129A THR* 3.6 11.0 - - - +
132A GLU* 3.7 7.8 + - - +
138A TYR* 3.2 11.6 + - + +
139A ASP* 1.3 77.0 - - - +
141A VAL* 1.3 67.3 + - - +
142A PRO* 3.6 14.7 - - - +
143A VAL* 3.2 22.1 + - - +
144A THR* 3.1 15.9 + - - -
313A LEU* 6.1 0.2 - - - +
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Residues in contact with VAL 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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38A LEU* 4.0 32.5 - - + -
99A VAL* 5.5 0.4 - - + -
101A PHE* 3.9 32.1 - - + -
106A ILE* 4.4 7.3 - - + +
109A GLN* 3.6 21.2 - - + +
124A MET* 4.2 25.6 - - + -
125A GLY 5.2 1.8 + - - +
126A ILE* 4.8 0.7 - - + -
140A ASN* 1.3 75.0 - - - +
142A PRO* 1.3 72.6 - - + +
144A THR* 3.2 4.2 + - - -
145A LEU* 3.1 27.5 + - + +
172A PHE* 4.9 2.9 - - + -
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Residues in contact with PRO 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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125A GLY 4.8 0.2 - - - +
126A ILE* 3.6 39.7 - - + +
140A ASN* 3.6 18.6 - - - +
141A VAL* 1.3 96.3 - - + +
143A VAL* 1.3 61.1 + - - +
145A LEU* 3.5 12.3 + - + +
146A LYS* 3.4 17.7 + - - +
151A ILE* 4.1 5.6 - - + +
154A ASN* 3.1 30.1 - - - +
156A TYR* 4.3 10.1 - - + -
172A PHE* 4.5 7.6 - - + -
313A LEU* 4.9 2.0 - - + -
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Residues in contact with VAL 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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129A THR* 3.9 18.6 - - + -
139A ASP* 3.5 33.0 - - + +
140A ASN* 3.2 22.7 + - - +
142A PRO* 1.3 76.4 - - - +
144A THR* 1.3 58.2 + - - +
146A LYS* 3.1 8.7 + - + +
147A LYS* 2.9 40.5 + - + +
154A ASN* 3.6 20.4 - - - +
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Residues in contact with THR 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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106A ILE* 4.0 13.2 - - + -
107A LYS 4.6 3.6 - - - +
108A ASN 5.8 0.4 - - - +
109A GLN* 2.7 30.6 + - + +
139A ASP* 3.7 16.5 + - - +
140A ASN 3.1 7.3 + - - -
141A VAL 3.7 3.8 - - - -
143A VAL* 1.3 77.7 - - - +
145A LEU* 1.3 63.6 + - - +
147A LYS* 4.4 6.5 - - + +
148A GLN* 2.9 56.2 + - + +
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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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3A VAL* 5.3 0.2 - - + -
101A PHE* 4.0 19.7 - - + -
104A ILE* 3.6 30.7 - - + -
106A ILE* 3.7 22.0 - - + -
141A VAL* 3.1 22.8 + - + +
142A PRO* 3.6 8.7 - - + +
143A VAL 3.3 0.2 - - - -
144A THR* 1.3 77.5 - - - +
146A LYS* 1.3 58.9 + - - +
148A GLN 3.8 0.3 + - - -
149A GLY 3.7 0.9 + - - -
150A ILE* 3.0 37.0 + - + +
151A ILE* 3.3 18.9 + - + -
172A PHE* 3.7 41.7 - - + -
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Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO 3.4 7.9 + - - +
143A VAL* 3.1 11.0 + - + +
145A LEU* 1.3 78.3 - - - +
147A LYS* 1.3 68.5 + - + +
149A GLY* 3.1 14.7 + - - -
151A ILE* 3.5 26.4 - - + +
152A ASN 3.8 17.9 - - - +
154A ASN* 3.9 14.6 - - + +
314A ASP* 2.7 37.0 + - - +
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Residues in contact with LYS 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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139A ASP* 2.8 37.5 + - - +
143A VAL* 2.9 31.1 + - + +
144A THR* 4.0 6.5 - - + +
146A LYS* 1.3 81.3 - - + +
148A GLN* 1.3 61.3 + - + +
149A GLY 3.2 2.8 + - - -
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Residues in contact with GLN 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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105A SER 4.5 0.7 - - - +
106A ILE* 3.5 10.9 - - + +
107A LYS* 3.0 53.1 + - - +
108A ASN* 5.9 0.2 - - - +
144A THR* 2.9 38.8 + - + +
145A LEU 4.6 1.6 - - - +
146A LYS 3.2 0.4 - - - -
147A LYS* 1.3 79.2 - - + +
149A GLY* 1.3 61.1 + - - +
150A ILE* 3.3 15.3 + - + +
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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