Contacts of the helix formed by residues 75 - 84 (chain A) in PDB entry 3L6D
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 ASP 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.3 1.2 - - - +
74A LEU* 1.3 95.1 - - + +
76A ASN* 1.3 64.2 + - - +
77A HIS* 3.3 21.2 + - + +
78A ALA* 2.9 33.7 + - - +
79A THR* 3.2 14.0 + - - -
101A THR* 3.8 14.9 - - - +
102A THR 4.5 6.1 - - - +
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Residues in contact with ASN 76 (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 ASP* 1.3 76.4 - - - +
77A HIS* 1.3 68.8 + - + +
79A THR* 3.2 8.6 + - - -
80A HIS* 3.1 46.5 + - - -
101A THR* 4.4 2.4 - - - +
102A THR 4.7 3.4 + - - -
103A ASN* 3.0 28.9 + - + +
107A GLU* 3.4 46.2 + - - +
111A LEU* 3.4 14.9 - - - +
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Residues in contact with HIS 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 ASP* 3.3 19.2 - - - +
76A ASN* 1.3 80.5 + - + +
78A ALA* 1.3 64.4 + - - +
80A HIS* 3.2 7.2 + - - +
81A GLU* 2.9 25.3 + - - +
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Residues in contact with ALA 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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73A LEU* 3.9 18.2 - - + -
74A LEU* 4.0 9.9 - - + +
75A ASP* 2.9 31.2 + - - +
77A HIS* 1.3 76.7 - - - +
79A THR* 1.3 56.9 + - - +
81A GLU* 3.4 16.9 + - - +
82A VAL* 2.9 33.8 + - + +
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Residues in contact with THR 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 PHE* 4.3 17.3 - - + -
73A LEU* 3.7 11.7 - - - +
75A ASP 3.2 11.9 + - - -
76A ASN* 3.2 11.9 + - - -
78A ALA* 1.3 75.6 - - - +
80A HIS* 1.3 58.8 + - - +
82A VAL* 3.4 3.3 + - - +
83A LEU* 3.0 42.7 + - + +
99A ASP* 4.7 4.0 - - - +
101A THR* 3.8 22.2 + - - +
111A LEU* 3.8 30.4 - - + +
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Residues in contact with HIS 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 ASN* 3.1 35.3 + - - +
77A HIS* 3.8 8.5 - - - +
79A THR* 1.3 76.9 - - - +
81A GLU* 1.3 59.1 + - - +
83A LEU* 3.1 5.0 + - + +
84A GLY* 2.9 27.7 + - - -
107A GLU 5.2 1.8 - - - -
110A ALA* 5.3 6.7 - - + +
111A LEU* 3.2 32.9 + - + +
114A LEU* 4.2 22.8 - - + +
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Residues in contact with GLU 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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40A ARG* 3.3 41.5 + - - +
77A HIS 2.9 15.2 + - - +
78A ALA* 3.5 16.5 - - - +
80A HIS* 1.3 76.4 - - - +
82A VAL* 1.3 60.3 + - - +
84A GLY* 3.5 2.2 + - - -
85A MSE 3.3 25.7 + - + +
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Residues in contact with VAL 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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15A ILE* 4.5 6.1 - - + -
38A TRP* 4.3 15.9 - - + -
40A ARG* 4.1 14.6 - - - +
59A VAL* 3.7 28.0 - - + -
71A PHE* 4.0 22.2 - - + -
73A LEU* 3.7 21.1 - - + -
78A ALA* 2.9 19.3 + - + +
79A THR 3.6 7.4 - - - +
81A GLU* 1.3 74.9 - - - +
83A LEU* 1.3 63.8 + - + +
84A GLY 3.1 0.2 - - - -
85A MSE 3.1 25.7 + - - +
88A VAL* 3.6 7.8 - - - +
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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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71A PHE* 3.9 27.8 - - + -
79A THR* 3.0 37.3 + - + +
80A HIS* 3.1 6.4 + - - +
82A VAL* 1.3 75.2 - - - +
84A GLY* 1.3 58.1 + - - +
85A MSE 3.4 0.6 - - - +
88A VAL* 3.7 31.6 - - + +
89A ALA* 4.3 8.3 + - - +
92A LEU* 4.0 21.9 - - + +
111A LEU* 4.4 11.0 - - + -
114A LEU* 4.1 36.6 - - + +
115A VAL* 4.8 9.6 - - + -
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Residues in contact with GLY 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 HIS 2.9 13.3 + - - -
81A GLU* 3.5 4.2 + - - -
82A VAL 3.1 0.2 - - - -
83A LEU* 1.3 75.7 - - - +
85A MSE 1.3 66.7 + - - +
86A PRO* 4.7 0.3 - - - +
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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