Contacts of the helix formed by residues 64 - 72 (chain O) in PDB entry 3L73
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 GLY 64 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58O GLU* 2.9 16.3 + - - -
63O LEU* 1.3 70.7 - - - +
65O THR* 1.3 61.7 + - - +
66O ALA 2.9 5.8 - - - -
67O HIS* 2.8 18.4 + - - +
68O LEU 3.0 10.7 + - - -
178O CYS* 3.7 32.0 - - - +
179O PRO* 4.1 3.0 - - - +
186O ILE* 3.8 8.3 - - - +
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Residues in contact with THR 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O GLU* 3.9 8.3 - - + -
62O ASN* 2.8 50.9 - - - +
63O LEU 3.0 5.1 + - - -
64O GLY* 1.3 76.1 - - - +
66O ALA* 1.3 62.2 + - - +
68O LEU* 4.1 0.9 - - - -
69O LEU* 3.1 23.7 + - - +
186O ILE* 3.9 21.1 - - - +
190O GLN* 3.7 21.6 + - - -
191O LEU* 3.6 13.7 + - - +
194O PHE* 3.9 15.1 - - + +
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Residues in contact with ALA 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O GLY* 4.0 9.4 - - - -
55O SER* 3.8 23.3 - - - +
58O GLU* 3.0 19.5 + - - +
64O GLY 2.8 0.8 + - - -
65O THR* 1.3 78.9 - - - +
67O HIS* 1.3 63.5 + - - +
69O LEU* 3.3 8.1 + - - +
70O ARG* 3.1 23.0 + - - +
105O MET* 4.7 9.8 - - - +
194O PHE* 4.3 16.6 - - + -
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Residues in contact with HIS 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O GLU* 4.2 0.6 + - - -
64O GLY* 2.8 10.4 + - - +
66O ALA* 1.3 80.1 - - - +
68O LEU* 1.3 58.2 + - - +
70O ARG* 2.9 56.9 + - - +
71O LEU* 3.2 8.1 + - + +
144O LEU* 3.6 33.6 - - + +
147O ASP* 3.0 24.9 + - - -
148O LYS* 4.4 3.8 - - + -
176O LEU 4.1 7.4 + - - +
177O TYR* 3.6 20.4 - + + -
178O CYS* 2.8 38.8 + - + +
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Residues in contact with LEU 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O GLY 3.0 3.5 + - - +
65O THR 4.3 3.4 - - - +
67O HIS* 1.3 78.7 - - - +
69O LEU* 1.3 63.0 + - - +
71O LEU* 3.1 3.9 + - + +
72O ALA* 2.9 21.5 + - + +
137O VAL* 4.5 4.5 - - + +
140O LEU* 4.1 26.2 - - + -
141O GLN* 3.9 28.7 - - + +
144O LEU* 3.8 23.1 - - + +
186O ILE* 3.4 52.9 - - + -
191O LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O THR 3.1 20.3 + - - +
66O ALA 3.4 5.6 - - - +
67O HIS 3.2 0.2 - - - -
68O LEU* 1.3 77.1 - - - +
70O ARG* 1.3 61.4 + - - +
72O ALA* 3.4 12.1 + - - +
73O SER* 3.8 3.6 + - - -
105O MET* 4.2 5.2 - - + -
107O TYR* 3.8 17.6 + - - +
132O PHE* 3.2 38.8 - - + -
191O LEU* 3.8 10.0 - - + +
194O PHE* 3.7 28.0 - - + -
195O VAL* 3.6 24.0 - - + -
199O PHE* 3.7 17.3 - - + -
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Residues in contact with ARG 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O ALA* 3.1 13.1 + - - +
67O HIS* 2.9 55.4 + - + +
69O LEU* 1.3 79.3 - - - +
71O LEU* 1.3 60.3 + - + +
72O ALA 3.4 0.2 + - - -
73O SER* 3.3 18.0 + - - -
98O VAL* 3.6 41.4 - - + +
100O SER* 3.2 28.3 + - - +
105O MET* 5.0 2.9 - - + -
107O TYR* 4.9 1.3 - - - -
147O ASP* 4.2 4.2 + - - -
176O LEU* 3.7 21.6 + - - +
177O TYR* 3.4 29.1 - - - -
66V ALA* 3.5 23.0 - - - +
67V GLY* 4.7 3.4 - - - +
68V ILE* 3.8 15.0 - - + +
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Residues in contact with LEU 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285N GLY* 5.6 1.9 - - - -
67O HIS* 3.2 17.5 + - + +
68O LEU* 3.1 7.2 + - + +
70O ARG* 1.3 79.1 - - + +
72O ALA* 1.3 57.3 + - - +
73O SER* 3.2 1.5 + - - -
74O PRO* 3.0 22.3 - - - +
140O LEU* 4.0 21.4 - - + +
143O GLN* 3.9 27.8 - - + -
144O LEU* 3.3 36.3 - - + +
147O ASP* 3.8 19.1 - - + +
68V ILE* 3.6 37.7 - - + +
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Residues in contact with ALA 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LEU* 2.9 16.4 + - + +
69O LEU* 3.6 12.3 - - - +
70O ARG 3.2 1.0 - - - -
71O LEU* 1.3 75.9 - - - +
73O SER* 1.3 64.0 + - - +
74O PRO* 3.2 4.5 - - - -
75O LEU* 3.1 38.3 + - + +
132O PHE* 4.3 18.2 - - + -
140O LEU* 3.6 12.5 - - + +
191O LEU* 5.1 5.6 - - + -
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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