Contacts of the helix formed by residues 76 - 92 (chain A) in PDB entry 3LHR
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 ASN 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.9 24.7 - - + +
54A LEU* 3.7 20.2 - - - +
74A PRO* 3.4 2.2 - - - +
75A GLU* 1.3 83.3 - - - +
77A GLY* 1.3 62.6 + - - +
78A GLU* 3.1 16.1 + - - +
79A GLU* 2.9 35.3 + - - +
80A ALA 3.1 16.8 + - - -
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Residues in contact with GLY 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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50A GLU* 3.5 12.5 + - - -
53A VAL* 5.5 1.6 - - - -
54A LEU* 4.2 20.3 - - - +
57A PHE* 5.4 0.4 - - - -
76A ASN* 1.3 73.1 - - - +
78A GLU* 1.3 65.4 + - - +
80A ALA* 3.2 5.3 + - - +
81A VAL* 3.0 29.7 + - - +
27B VAL* 4.1 20.3 - - - +
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Residues in contact with GLU 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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50A GLU* 4.8 2.2 - - - +
76A ASN* 3.2 12.3 - - - +
77A GLY* 1.3 76.5 - - - +
79A GLU* 1.3 62.2 + - + +
81A VAL* 3.3 4.9 + - - +
82A THR* 3.0 27.9 + - - -
24B ARG* 2.7 33.4 + - - +
27B VAL* 4.4 3.3 - - - +
31B ARG* 2.5 37.0 + - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY 4.3 9.4 + - - -
74A PRO* 3.4 13.1 - - + +
75A GLU* 2.8 42.2 + - - +
76A ASN* 2.9 29.5 + - - +
78A GLU* 1.3 79.1 - - + +
80A ALA* 1.3 62.5 + - - +
82A THR* 3.4 8.3 + - - -
83A VAL* 3.1 26.6 + - + +
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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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54A LEU* 3.7 28.0 - - + -
57A PHE* 3.8 22.0 - - + -
69A VAL* 4.1 8.5 - - + +
74A PRO* 3.5 15.1 - - + +
76A ASN 3.1 4.0 + - - -
77A GLY 3.2 8.9 + - - +
79A GLU* 1.3 76.6 - - - +
81A VAL* 1.3 63.8 + - - +
83A VAL* 3.1 16.6 + - - +
84A LEU* 3.1 16.8 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.4 1.8 - - + -
77A GLY 3.0 18.8 + - - +
78A GLU* 3.7 8.3 - - - +
79A GLU 3.2 0.2 - - - -
80A ALA* 1.3 75.9 - - - +
82A THR* 1.3 52.4 + - - +
84A LEU* 3.1 6.4 + - - +
85A GLU* 2.7 43.9 + - - +
23B PRO* 3.8 23.6 - - + +
24B ARG* 3.2 51.6 - - - +
27B VAL* 3.5 25.4 - - + -
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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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78A GLU 3.0 14.0 + - - -
79A GLU* 3.5 11.8 - - - -
81A VAL* 1.3 72.6 - - - +
83A VAL* 1.3 56.5 + - + +
85A GLU* 3.7 8.2 + - + +
86A ASP* 2.6 54.3 + - - +
24B ARG* 3.6 12.9 + - - +
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Residues in contact with VAL 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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68A TRP* 3.5 31.8 + - + +
69A VAL* 4.1 11.9 - - + -
72A HIS* 3.8 37.0 - - + +
74A PRO* 4.9 7.2 - - + -
79A GLU* 3.1 22.9 + - + +
80A ALA* 3.3 12.3 - - - +
82A THR* 1.3 76.8 - - + +
84A LEU* 1.3 55.6 + - - +
86A ASP* 3.4 8.4 + - - +
87A LEU* 3.0 27.0 + - - +
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Residues in contact with LEU 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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57A PHE* 3.5 37.0 - - + -
61A LEU* 3.9 14.6 - - + -
65A LEU* 4.1 36.3 - - + +
68A TRP* 5.3 0.9 - - + -
69A VAL* 3.7 20.9 - - + -
80A ALA 3.1 8.3 + - - +
81A VAL* 3.1 7.2 + - - +
83A VAL* 1.3 74.1 - - - +
85A GLU* 1.3 60.4 + - - +
87A LEU* 3.3 9.1 + - + +
88A GLU* 2.8 32.1 + - - +
17B TYR* 4.0 4.7 - - - +
23B PRO* 3.8 21.3 - - + -
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Residues in contact with GLU 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 VAL* 2.7 32.3 + - + +
82A THR* 3.7 7.8 + - + +
84A LEU* 1.3 72.5 - - - +
86A ASP* 1.3 63.6 + - - +
88A GLU* 3.5 16.2 + - - +
89A SER* 3.1 27.3 + - - -
23B PRO* 4.9 9.4 - - + +
24B ARG* 3.6 33.5 + - - +
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Residues in contact with ASP 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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82A THR* 2.6 41.8 + - - +
83A VAL* 3.7 7.9 - - - +
85A GLU* 1.3 72.2 - - - +
87A LEU* 1.3 64.3 + - - +
89A SER* 3.2 6.8 + - - -
90A GLU* 3.0 25.2 + - - +
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Residues in contact with LEU 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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65A LEU* 3.6 30.3 - - + -
68A TRP* 3.8 59.2 - - + +
83A VAL 3.0 17.1 + - - +
84A LEU* 3.7 9.0 - - + +
86A ASP* 1.3 74.4 - - - +
88A GLU* 1.3 67.1 + - - +
90A GLU* 3.1 9.3 + - + +
91A LEU* 2.9 56.3 + - + +
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Residues in contact with GLU 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 LEU* 2.8 21.4 + - - +
85A GLU* 3.5 18.4 - - - +
87A LEU* 1.3 74.5 - - - +
89A SER* 1.3 64.8 + - - +
91A LEU* 3.2 6.3 + - - -
92A ASP* 3.1 45.4 + - - +
23B PRO* 5.6 6.2 - - - +
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Residues in contact with SER 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 GLU 3.1 15.8 + - - -
86A ASP* 3.8 6.1 - - - -
87A LEU 3.1 0.8 - - - -
88A GLU* 1.3 80.2 - - - +
90A GLU* 1.3 60.0 + - - +
92A ASP* 3.4 18.5 + - - +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TRP* 5.5 8.4 - - - -
86A ASP* 3.0 16.8 + - - +
87A LEU* 3.1 11.1 + - + +
89A SER* 1.3 75.0 - - - +
91A LEU* 1.3 64.2 + - + +
92A ASP 3.5 1.7 + - - -
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Residues in contact with LEU 91 (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 LEU* 6.3 0.4 - - + -
87A LEU* 2.9 46.2 + - + +
88A GLU* 3.8 6.1 - - - +
90A GLU* 1.3 80.4 - - + +
92A ASP* 1.3 70.4 + - - +
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Residues in contact with ASP 92 (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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88A GLU* 3.1 35.5 + - - +
89A SER* 3.4 14.0 + - - +
90A GLU 5.0 1.1 - - - -
91A LEU* 1.3 89.2 - - - +
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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