Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 3D77
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 LEU 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TRP* 3.5 45.3 - - + +
74A LEU* 3.8 19.1 - - + -
75A PRO* 2.9 21.0 + - + +
77A GLN* 1.3 79.1 - - - +
79A GLN* 1.3 58.4 + - - +
80A GLU 3.5 1.3 - - - -
81A ARG* 3.4 29.2 + - + +
82A ALA* 2.9 27.9 + - - +
114A ASP* 4.5 4.0 - - + +
115A VAL* 3.7 35.7 - - + -
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Residues in contact with GLN 79 (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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71A LEU* 3.0 36.6 + - + +
72A GLY* 4.3 6.5 + - - -
74A LEU* 2.9 27.5 + - + +
75A PRO 3.4 13.4 + - - +
76A ASP* 3.5 22.9 + - - +
78A LEU* 1.3 75.7 - - - +
80A GLU* 1.3 60.8 + - - +
82A ALA* 3.7 5.9 - - - +
83A GLN* 2.8 31.9 + - - +
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Residues in contact with GLU 80 (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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76A ASP 4.6 7.5 + - - +
77A GLN* 5.2 6.1 - - - +
78A LEU 3.5 0.6 - - - -
79A GLN* 1.3 77.3 - - + +
81A ARG* 1.3 57.8 + - - +
83A GLN* 3.7 7.7 - - - +
84A SER* 2.9 29.0 + - - -
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Residues in contact with ARG 81 (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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77A GLN 4.1 14.3 + - - +
78A LEU* 3.4 21.9 + - + +
79A GLN 3.3 0.2 - - - -
80A GLU* 1.3 79.7 - - - +
82A ALA* 1.3 57.7 + - - +
84A SER* 3.4 7.9 + - - -
85A VAL* 3.0 27.9 + - - +
112A ALA* 4.1 23.3 - - + +
114A ASP* 3.4 38.0 + - - +
115A VAL* 4.5 3.5 - - + +
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Residues in contact with ALA 82 (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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71A LEU* 4.0 4.5 - - + -
74A LEU* 3.5 31.9 - - + -
78A LEU* 2.9 19.0 + - + +
79A GLN* 3.7 3.6 - - - +
81A ARG* 1.3 74.5 - - - +
83A GLN* 1.3 59.5 + - - +
85A VAL* 3.3 9.4 - - - +
86A MET* 2.9 37.5 + - + +
115A VAL* 4.1 18.1 - - + +
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Residues in contact with GLN 83 (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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67A GLU* 3.8 21.3 + - - +
68A ASP* 5.5 2.2 + - - -
71A LEU* 3.8 25.5 - - + +
79A GLN 2.8 22.0 + - - +
80A GLU* 3.7 7.3 - - - +
82A ALA* 1.3 71.4 - - - +
84A SER* 1.3 62.5 + - - +
86A MET 3.4 1.0 + - - -
87A GLY* 3.0 19.8 + - - -
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Residues in contact with SER 84 (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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80A GLU 2.9 17.8 + - - -
81A ARG* 3.4 10.8 - - - -
83A GLN* 1.3 76.7 - - - +
85A VAL* 1.3 63.3 + - - +
87A GLY* 3.1 11.3 + - - -
88A LYS* 3.4 10.7 + - - +
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Residues in contact with VAL 85 (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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81A ARG 3.0 15.5 + - - +
82A ALA* 3.3 15.7 - - - +
84A SER* 1.3 76.7 + - - +
86A MET* 1.3 69.5 + - + +
88A LYS* 3.1 9.8 + - + +
89A CYS* 2.8 39.0 + - - +
108A VAL* 3.9 28.7 - - + -
111A SER* 3.6 31.6 - - - -
112A ALA* 4.0 15.3 - - + -
115A VAL* 4.5 4.9 - - + -
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Residues in contact with MET 86 (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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65A VAL* 5.4 0.4 - - - -
67A GLU* 3.4 30.4 - - + +
70A MET* 3.7 30.5 - - + +
71A LEU* 5.4 2.9 - - + -
74A LEU* 6.6 0.4 - - + -
82A ALA* 2.9 23.5 + - + +
83A GLN* 5.0 0.2 - - - -
84A SER 3.2 0.2 - - - -
85A VAL* 1.3 79.0 - - + +
87A GLY* 1.3 64.1 + - - +
89A CYS 4.2 1.3 - - - +
90A LEU* 3.1 49.5 + - + +
104A LEU* 4.1 13.7 - - + -
108A VAL* 3.8 25.4 - - + -
115A VAL* 4.8 9.6 - - + -
116A TRP* 4.3 14.4 - - + -
121A NBB 5.0 1.3 - - + -
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Residues in contact with GLY 87 (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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67A GLU* 4.5 2.9 + - - -
83A GLN 3.0 14.5 + - - -
84A SER* 3.1 5.9 + - - -
86A MET* 1.3 78.2 - - - +
88A LYS* 1.3 60.9 + - - +
90A LEU 3.8 8.8 - - - +
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Residues in contact with LYS 88 (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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84A SER 3.4 9.3 + - - +
85A VAL* 3.1 10.0 + - + +
87A GLY* 1.3 81.5 - - - +
89A CYS* 1.3 64.3 + - - +
90A LEU 3.5 3.9 + - - +
107A CYS* 4.4 11.1 - - - -
110A GLU* 5.5 1.0 - - - +
111A SER* 2.6 38.1 + - - +
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Residues in contact with CYS 89 (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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85A VAL* 2.8 28.9 + - - +
86A MET* 3.4 2.0 + - - -
88A LYS* 1.3 83.5 - - - +
90A LEU* 1.3 60.5 + - - +
91A PRO 3.7 8.8 - - - +
92A THR* 4.5 2.6 + - - -
104A LEU* 3.8 27.2 - - + +
107A CYS* 2.0 65.8 - - + +
108A VAL* 3.6 5.2 - - + -
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Residues in contact with LEU 90 (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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65A VAL* 3.8 29.6 - - + +
67A GLU* 3.9 30.7 - - + +
86A MET* 3.1 37.9 + - + +
87A GLY 3.8 14.2 - - - +
88A LYS 4.1 3.9 - - - +
89A CYS* 1.3 80.7 - - - +
91A PRO* 1.3 66.7 - - + +
92A THR* 3.8 30.7 - - + +
104A LEU* 4.1 9.0 - - + -
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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