Contacts of the helix formed by residues 64 - 72 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.8 16.6 + - - -
63B LEU* 1.3 71.0 - - - +
65B THR* 1.3 55.2 + - - -
66B ALA 2.9 6.1 - - - -
67B HIS* 2.8 24.2 + - - +
68B LEU 2.9 11.1 + - - -
175B PRO 6.1 0.4 - - - -
178B CYS* 3.8 30.9 - - - +
179B PRO* 4.1 3.2 - - - +
186B ILE* 3.7 8.5 - - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 3.8 8.1 - - + -
62B ASN* 2.7 49.8 - - - +
63B LEU 3.0 5.1 + - - -
64B GLY* 1.3 74.8 - - - +
66B ALA* 1.3 63.3 + - - +
68B LEU* 4.1 1.8 - - - -
69B LEU* 3.2 24.8 + - - +
186B ILE* 3.8 20.3 - - - +
190B GLN* 3.7 22.6 + - - +
191B LEU* 3.5 14.2 + - - +
194B PHE* 3.9 13.4 - - + +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY* 4.0 9.2 - - - -
55B SER* 3.8 24.5 - - - +
58B GLU* 2.9 19.3 + - - +
64B GLY 2.9 0.6 - - - -
65B THR* 1.3 79.1 - - - +
67B HIS* 1.3 63.9 + - - +
69B LEU* 3.2 8.4 + - - +
70B ARG* 3.1 23.9 + - - +
105B MET* 4.8 9.3 - - - +
194B PHE* 4.3 15.9 - - + -
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 4.2 0.4 + - - -
64B GLY* 2.8 10.7 + - - +
66B ALA* 1.3 78.8 - - - +
68B LEU* 1.3 56.8 + - - +
70B ARG* 2.9 54.9 + - - +
71B LEU* 3.3 8.7 + - + +
144B LEU* 3.5 35.9 - - + +
147B ASP* 2.9 27.4 + - - -
148B LYS* 4.4 3.6 - - + -
176B LEU 4.1 7.8 + - - +
177B TYR* 3.5 17.0 - + + -
178B CYS* 2.7 39.3 + - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLY 2.9 7.1 + - - +
65B THR 4.3 2.7 - - - +
67B HIS* 1.3 77.6 - - - +
69B LEU* 1.3 63.1 + - - +
71B LEU* 3.3 2.8 + - + +
72B ALA* 3.0 21.8 + - + +
137B VAL* 4.6 5.2 - - + +
140B LEU* 4.0 28.0 - - + -
141B GLN* 3.9 26.9 - - + +
144B LEU* 3.8 22.6 - - + +
186B ILE* 3.4 52.5 - - + -
191B LEU* 4.0 20.0 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR 3.2 19.6 + - - +
66B ALA 3.2 6.5 + - - +
67B HIS 3.1 0.6 - - - -
68B LEU* 1.3 76.9 - - - +
70B ARG* 1.3 62.5 + - - +
72B ALA* 3.4 10.4 + - - +
73B SER 3.8 4.3 + - - -
105B MET* 4.3 4.5 - - + -
107B TYR* 3.7 19.2 + - - +
132B PHE* 3.1 39.5 - - + -
191B LEU* 3.8 8.7 - - + +
194B PHE* 3.6 33.4 - - + -
195B VAL* 3.7 18.2 - - + -
199B PHE* 3.8 17.0 - - + -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.1 12.0 + - - +
67B HIS* 2.9 55.1 + - - +
69B LEU* 1.3 80.2 - - - +
71B LEU* 1.3 60.7 + - + +
72B ALA 3.4 0.3 + - - -
73B SER* 3.2 18.9 + - - -
98B VAL* 3.4 42.6 - - + +
100B SER* 3.2 27.9 + - - +
105B MET* 4.9 3.6 - - + +
107B TYR* 4.8 1.6 - - - -
147B ASP* 4.3 2.6 + - - -
176B LEU* 3.7 21.0 + - - +
177B TYR* 3.4 28.9 - - - -
66I ALA* 3.5 23.2 - - - +
67I GLY 4.7 2.2 - - - +
68I ILE* 3.7 17.8 - - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLY* 5.7 1.6 - - - -
67B HIS* 3.3 17.9 + - + +
68B LEU* 3.3 7.7 + - + +
70B ARG* 1.3 79.8 - - + +
72B ALA* 1.3 57.7 + - - +
73B SER 3.2 0.4 - - - -
74B PRO* 3.2 20.9 - - - +
140B LEU* 3.8 21.6 - - + +
143B GLN* 3.9 26.5 - - + -
144B LEU* 3.4 31.4 - - + +
147B ASP* 3.8 22.2 - - + +
68I ILE* 3.4 37.8 - - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.0 17.2 + - + +
69B LEU* 3.6 12.6 - - - +
70B ARG 3.2 0.8 - - - -
71B LEU* 1.3 75.0 - - - +
73B SER* 1.3 65.9 + - - +
74B PRO* 3.2 4.7 - - - -
75B LEU* 3.0 38.5 + - + +
132B PHE* 4.3 18.3 - - + -
140B LEU* 3.5 13.5 - - + -
191B 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