Contacts of the helix formed by residues 76 - 92 (chain A) in PDB entry 4LTS
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 THR 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS* 4.4 19.7 - - + +
75A VAL* 1.3 79.9 - - - +
77A LYS* 1.3 65.2 + - - +
78A GLU* 3.4 15.5 + - - +
79A LYS* 3.0 41.1 + - + +
80A ILE* 3.0 24.9 + - - +
105A LEU* 4.0 12.8 - - - -
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Residues in contact with LYS 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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76A THR* 1.3 73.0 - - - +
78A GLU* 1.3 73.2 + - - +
80A ILE* 3.3 7.7 + - - +
81A GLN* 3.0 28.1 + - - +
102A ASN* 5.3 4.0 - - - +
105A LEU* 3.7 23.2 - - + +
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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
----------------------------------------------------------
76A THR* 3.2 13.9 + - - +
77A LYS* 1.3 95.8 + - - +
79A LYS* 1.3 58.9 + - + +
81A GLN* 3.3 6.5 + - - +
82A GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.3 29.1 + - - -
9A PHE* 2.9 29.6 + - - -
10A ASN* 3.1 38.0 + - + +
11A ILE 5.1 0.8 - - - +
12A LEU* 4.0 6.9 - - + +
73A LYS 4.9 3.0 + - - -
74A VAL* 3.6 32.3 + - - +
76A THR* 3.0 34.6 + - + +
78A GLU* 1.3 73.6 - - + +
80A ILE* 1.3 64.9 + - - +
82A GLU* 4.3 4.7 - - - +
83A ALA* 3.0 23.0 + - - +
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Residues in contact with ILE 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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12A LEU* 3.7 15.0 - - + -
75A VAL* 3.7 28.7 - - + -
76A THR 3.0 16.9 + - - +
77A LYS* 3.6 7.6 - - - +
79A LYS* 1.3 76.5 - - - +
81A GLN* 1.3 59.5 + - - +
83A ALA* 3.4 3.1 + - - +
84A LYS* 2.9 26.8 + - + +
96A PHE* 3.8 10.2 - - + -
98A GLU* 3.9 32.8 - - + +
101A TRP* 3.9 3.6 - - + +
102A ASN* 3.9 40.8 - - - +
105A LEU* 4.0 9.9 - - + -
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Residues in contact with GLN 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 LYS 3.0 17.5 + - - +
78A GLU* 3.8 6.7 - - - +
80A ILE* 1.3 75.4 - - - +
82A GLU* 1.3 65.5 + - - +
84A LYS* 3.3 25.7 + - - +
85A ASP* 2.9 61.2 + - - +
98A GLU* 5.0 4.2 - - - +
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Residues in contact with GLU 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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8A GLU 5.3 2.9 - - - +
10A ASN* 2.9 22.6 + - - +
13A LEU* 3.7 22.5 - - + +
78A GLU 2.9 17.2 + - - +
79A LYS* 3.7 7.5 - - - +
81A GLN* 1.3 75.5 - - - +
83A ALA* 1.3 63.8 + - - +
85A ASP* 3.1 8.8 + - - +
86A VAL* 3.0 33.3 + - + +
225B ALA* 5.7 4.2 - - - +
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Residues in contact with ALA 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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10A ASN* 4.3 0.8 - - - +
12A LEU* 3.6 31.2 - - + -
13A LEU* 4.0 16.8 - - + -
79A LYS 3.0 17.8 + - - +
80A ILE 3.8 3.4 - - - +
82A GLU* 1.3 75.5 - - - +
84A LYS* 1.3 63.6 + - - +
86A VAL* 3.2 1.2 + - - +
87A TYR* 2.9 39.0 + - + -
96A PHE* 3.9 11.0 - - + -
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Residues in contact with LYS 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 ILE 2.9 17.6 + - - +
81A GLN* 3.5 26.9 + - - +
82A GLU 3.2 0.2 - - - -
83A ALA* 1.3 77.4 - - - +
85A ASP* 1.3 63.2 + - - +
87A TYR* 3.5 1.0 + - - +
88A LYS* 3.1 25.8 + - + +
96A PHE* 3.8 25.7 - - + +
98A GLU* 2.8 39.6 + - - +
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Residues in contact with ASP 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 GLN* 2.9 48.7 + - - +
82A GLU* 3.6 9.5 - - - +
84A LYS* 1.3 78.0 - - - +
86A VAL* 1.3 64.9 + - + +
88A LYS* 3.6 11.6 + - - +
89A GLU* 3.6 19.6 + - - +
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Residues in contact with VAL 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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13A LEU* 4.0 32.3 - - + -
82A GLU* 3.0 28.0 + - + +
83A ALA 3.8 2.9 - - - +
85A ASP* 1.3 77.0 - - + +
87A TYR* 1.3 65.4 + - + +
89A GLU* 3.1 5.9 + - - +
90A HIS* 2.8 24.7 + - + +
221B VAL* 4.8 1.8 - - + -
224B LEU* 3.8 30.7 - - + -
237B VAL* 4.4 10.1 - - + +
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Residues in contact with TYR 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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12A LEU 2.7 29.1 + - - -
13A LEU* 3.6 18.0 - - + +
15A THR* 4.1 5.5 - - - +
17A SER* 5.1 0.4 - - - -
20A VAL* 3.5 27.5 - - + +
83A ALA* 2.9 32.4 + - + +
84A LYS 4.2 2.2 - - - +
86A VAL* 1.3 75.4 - - + +
88A LYS* 1.3 65.6 + - - +
90A HIS* 4.1 11.4 - + + -
91A PHE* 2.9 52.1 + + + +
93A ASP 3.6 2.4 - - - +
94A ASP 6.3 0.7 - - - -
95A VAL* 6.1 0.2 - - + -
96A PHE* 3.7 36.1 - + + +
147A TRP* 4.7 0.2 - + - -
221B VAL* 4.0 29.7 - - + +
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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 LYS* 3.1 19.7 + - + +
85A ASP* 3.7 8.7 - - - +
86A VAL 3.2 0.2 - - - -
87A TYR* 1.3 75.7 - - - +
89A GLU* 1.3 72.5 + - - +
92A GLN* 3.0 28.2 + - - -
93A ASP* 3.3 17.4 + - - +
94A ASP* 2.4 40.0 + - - +
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Residues in contact with GLU 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 ASP 3.6 13.9 - - - +
86A VAL* 3.1 6.5 + - - +
88A LYS* 1.3 94.3 - - - +
90A HIS* 1.3 64.2 + - - +
92A GLN* 2.7 34.4 + - - +
236B PRO* 3.7 30.7 - - + +
237B VAL* 3.8 22.4 - - + -
240B TYR* 3.5 9.9 - - - -
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Residues in contact with HIS 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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17A SER* 2.6 35.8 + - - -
86A VAL 2.8 17.4 + - - +
87A TYR* 4.0 15.5 - + + +
89A GLU* 1.3 76.9 - - - +
91A PHE* 1.3 71.9 + + - +
218B THR* 3.2 27.7 + - + -
221B VAL* 4.6 2.4 - - + +
224B LEU* 3.7 22.2 - - + +
237B VAL* 4.1 3.1 - - + +
239B GLY 2.8 28.8 + - - +
240B TYR* 3.3 28.5 - - - +
241B SER* 3.1 27.0 + - - +
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Residues in contact with PHE 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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17A SER* 3.2 33.9 - - - -
20A VAL* 3.9 13.9 - - + -
21A THR* 4.0 15.0 - - + -
87A TYR* 2.9 51.4 + + + +
90A HIS* 1.3 78.8 - + - +
92A GLN* 1.3 71.0 + - - +
93A ASP* 3.6 21.2 - - + +
95A VAL* 3.9 18.2 - - + -
241B SER* 3.6 26.1 - - - +
242B VAL* 3.9 31.5 - - - +
243B PRO* 4.3 6.1 - - + +
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Residues in contact with GLN 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 LYS* 3.0 13.9 + - - -
89A GLU* 2.7 42.5 + - - +
91A PHE* 1.3 80.2 - - - +
93A ASP* 1.3 59.9 + - - +
240B TYR* 4.0 21.7 + - + -
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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