Contacts of the helix formed by residues 76 - 86 (chain A) in PDB entry 3LB2
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL 5.4 0.4 + - - -
69A ARG* 3.9 39.5 - - + +
70A ALA* 4.9 1.4 - - - +
74A VAL 5.7 0.9 - - - +
75A PRO* 1.3 76.4 - - - +
77A ALA* 1.3 63.8 + - - +
78A SER* 3.6 21.3 - - - +
79A ASP* 3.0 35.7 + - - +
80A ALA* 3.2 12.0 + - - +
130A ALA* 5.6 0.4 - - - -
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Residues in contact with ALA 77 (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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75A PRO 3.6 3.6 + - - -
76A LEU* 1.3 72.9 - - - +
78A SER* 1.3 57.5 + - - +
80A ALA* 3.2 9.1 + - - +
81A ASN* 2.9 29.3 + - - +
130A ALA* 5.2 5.4 - - + -
133A SER* 5.9 2.9 - - - +
134A ALA* 5.0 2.1 - - - +
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Residues in contact with SER 78 (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 LEU* 3.6 21.5 - - - +
77A ALA* 1.3 78.7 - - - +
79A ASP* 1.3 62.3 + - - +
81A ASN* 3.4 7.3 + - - +
82A THR* 3.0 30.4 + - - -
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Residues in contact with ASP 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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62A LEU* 5.6 0.7 - - - +
66A VAL* 3.8 36.9 - - + +
69A ARG* 2.9 46.6 + - - +
75A PRO* 5.3 0.2 - - + -
76A LEU* 3.0 26.9 + - + +
78A SER* 1.3 82.9 + - - +
80A ALA* 1.3 65.1 + - - +
82A THR* 3.3 11.2 + - - -
83A LEU* 3.2 27.1 + - - +
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Residues in contact with ALA 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 LEU 3.2 8.9 + - - +
77A ALA* 3.2 8.9 + - - +
79A ASP* 1.3 75.3 - - - +
81A ASN* 1.3 63.3 + - - +
83A LEU* 3.1 6.6 + - - +
84A VAL* 3.0 26.8 + - - +
127A LEU* 4.4 11.0 - - + +
130A ALA* 3.5 46.2 - - + +
131A LEU* 3.6 12.0 - - + +
134A ALA* 4.6 0.4 - - + -
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Residues in contact with ASN 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 ALA 2.9 16.1 + - - +
78A SER* 3.7 7.4 - - - +
79A ASP 3.2 0.2 - - - -
80A ALA* 1.3 74.9 - - - +
82A THR* 1.3 66.4 + - - +
84A VAL* 3.1 2.5 + - - +
85A GLN* 2.9 61.0 + - - +
134A ALA* 3.6 28.2 + - + +
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Residues in contact with THR 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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62A LEU* 4.8 16.4 - - + -
78A SER 3.0 15.3 + - - -
79A ASP* 3.3 14.9 + - - -
81A ASN* 1.3 74.5 - - - +
83A LEU* 1.3 64.1 + - + +
85A GLN* 3.4 4.7 + - - +
86A MET* 3.1 40.6 + - + +
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Residues in contact with LEU 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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62A LEU* 3.9 19.1 - - + -
66A VAL* 5.0 9.0 - - + -
79A ASP 3.5 13.7 - - - +
80A ALA 3.1 7.4 + - - +
82A THR* 1.3 78.7 - - + +
84A VAL* 1.3 59.6 + - - +
86A MET* 3.7 4.0 + - - -
89A HIS* 2.8 43.9 + - + +
97A PHE* 4.6 5.4 - - + -
127A LEU* 4.3 23.3 - - + -
131A LEU* 3.9 13.0 - - + -
136A MET* 4.4 2.9 - - - +
139A HEM 3.7 52.3 - - + -
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Residues in contact with VAL 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 ALA 3.0 15.3 + - - +
81A ASN* 3.1 8.5 + - - +
83A LEU* 1.3 77.6 - - - +
85A GLN* 1.3 69.8 + - - +
86A MET 3.6 5.2 + - - +
89A HIS* 4.6 8.0 - - - +
90A SER* 5.3 2.3 - - - -
131A LEU* 3.7 34.5 - - + +
134A ALA* 3.8 27.4 - - + +
135A GLY 4.3 2.2 - - - -
136A MET* 3.9 31.0 - - + +
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Residues in contact with GLN 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 ASN* 2.9 48.0 + - - +
82A THR* 4.1 4.3 - - - +
84A VAL* 1.3 88.2 - - - +
86A MET* 1.3 66.5 + - - +
87A LYS* 3.2 3.8 + - - -
134A ALA 4.3 3.8 + - - -
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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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62A LEU* 4.6 8.7 - - - -
82A THR* 3.1 28.9 + - + +
83A LEU* 3.9 19.1 - - - +
84A VAL 3.4 2.7 - - - +
85A GLN* 1.3 77.0 - - - +
87A LYS* 1.3 59.5 + - - +
88A GLN* 3.9 19.3 - - - +
89A HIS* 2.9 47.9 + - + +
90A SER* 3.5 4.7 + - - -
139A HEM 3.5 49.4 - - + +
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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