Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 3THY
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 LYS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASP* 4.7 3.8 + - - -
40A GLY 2.9 28.3 + - - -
41A ASP* 4.0 20.3 + - - +
43A TYR* 3.5 33.2 + - + +
80A LEU 3.9 0.2 + - - -
81A SER* 1.3 71.7 - - - +
83A MET* 1.3 67.9 + - + +
85A PHE* 3.6 8.1 - - + +
86A GLU* 2.9 27.1 + - - +
264B TYR* 5.7 3.1 - - - +
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Residues in contact with MET 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.5 9.6 - - - +
82A LYS* 1.3 81.4 - - + +
84A ASN* 1.3 63.2 + - - +
86A GLU* 3.3 4.7 + - - +
87A SER* 3.1 20.4 + - - -
258B ALA 4.9 2.0 - - - +
262B ASN* 3.1 57.1 - - + +
263B ILE* 3.9 13.0 - - - +
264B TYR* 3.8 39.7 - - + +
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Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 4.1 5.6 - - + +
58A PHE* 3.3 30.9 - - - -
79A VAL 5.0 0.2 + - - -
80A LEU* 3.5 18.6 - - + -
81A SER* 3.0 21.6 + - - +
83A MET* 1.3 78.3 - - - +
85A PHE* 1.3 65.3 + - - +
87A SER* 3.0 7.1 + - - -
88A PHE* 2.8 25.1 + - - +
261B LEU 3.7 7.5 + - - +
262B ASN* 3.5 8.1 - - - +
280B ARG* 5.3 1.8 - - - +
284B HIS* 5.9 1.8 - - - -
287B ARG* 3.2 30.3 + - - +
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Residues in contact with PHE 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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36A LEU* 3.4 36.1 - - + -
43A TYR* 3.4 63.5 - + + -
80A LEU* 3.9 14.9 - - + +
81A SER 2.6 19.7 + - - +
82A LYS* 3.6 5.4 - - + +
84A ASN* 1.3 71.7 - - - +
86A GLU* 1.3 77.4 + - - +
88A PHE* 3.3 2.8 + - - +
89A VAL* 3.0 35.4 + - + +
102A VAL* 4.2 5.2 - - + -
121A TYR* 3.9 12.1 - - - -
131A PHE* 3.8 27.6 - + - -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS 2.9 17.2 + - - +
83A MET* 3.6 4.9 - - - +
85A PHE* 1.3 95.2 - - - +
87A SER* 1.3 65.6 + - - +
89A VAL* 3.2 3.7 + - - +
90A LYS* 3.0 25.0 + - + +
131A PHE* 3.6 24.8 - - - +
133A ASP* 3.0 34.8 - - + +
134A ILE* 4.7 6.5 - - + +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 5.7 1.8 - - - -
83A MET 3.1 7.0 + - - -
84A ASN* 3.0 7.1 + - - -
86A GLU* 1.3 79.9 - - - +
88A PHE* 1.3 60.9 + - - +
90A LYS* 3.5 9.9 - - - +
91A ASP* 3.2 21.7 + - - +
262B ASN* 3.2 33.6 + - - -
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.5 5.2 - - + -
36A LEU* 4.1 23.3 - - + -
45A ALA* 5.6 0.4 - - + -
49A ASP 5.0 1.3 - - - -
52A LEU* 4.1 11.2 - - + -
53A ALA* 3.7 31.9 - - + -
56A GLU* 3.7 30.7 - - + -
57A VAL* 3.3 28.4 - - + +
80A LEU* 4.1 18.2 - - + -
84A ASN 2.8 19.8 + - - +
85A PHE 3.7 3.4 - - - +
87A SER* 1.3 69.6 - - - +
89A VAL* 1.3 60.5 + - - +
91A ASP* 3.3 9.9 + - - +
92A LEU* 3.0 60.9 + - + +
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Residues in contact with VAL 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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36A LEU* 3.7 29.4 - - + -
85A PHE* 3.0 34.6 + - + +
86A GLU 3.6 3.6 - - - +
88A PHE* 1.3 72.0 - - - +
90A LYS* 1.3 66.8 + - - +
92A LEU* 3.2 8.7 + - + +
93A LEU* 3.0 43.5 + - + +
100A VAL* 4.6 12.1 - - + -
131A PHE* 3.6 31.2 - - + -
134A ILE* 4.0 4.5 - - + -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 3.0 14.3 + - + +
87A SER* 3.5 13.2 - - - +
89A VAL* 1.3 77.5 - - - +
91A ASP* 1.3 63.1 + - - +
94A LEU* 2.9 56.8 + - + +
134A ILE* 3.6 29.4 - - + +
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Residues in contact with ASP 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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56A GLU* 3.0 36.4 - - - +
87A SER 3.2 11.0 + - - +
88A PHE* 3.3 14.1 + - - +
90A LYS* 1.3 78.4 - - - +
92A LEU* 1.3 64.7 + - - +
95A VAL* 2.9 49.9 + - + +
96A ARG* 3.4 10.0 + - - +
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Residues in contact with LEU 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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34A VAL* 4.1 11.9 - - + -
36A LEU* 5.1 0.7 - - + -
52A LEU* 4.0 17.3 - - + -
56A GLU* 5.4 0.4 - - + -
88A PHE* 3.0 52.6 + - + +
89A VAL* 3.2 11.4 + - + +
91A ASP* 1.3 77.3 - - - +
93A LEU* 1.3 54.3 + - - +
96A ARG* 3.6 13.5 - - + -
97A GLN 2.9 12.3 + - - -
98A TYR* 2.7 61.2 + - + -
100A VAL* 3.8 26.0 - - + -
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Residues in contact with LEU 93 (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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89A VAL* 3.0 38.2 + - + +
90A LYS* 4.0 1.3 - - - +
92A LEU* 1.3 75.2 - - - +
94A LEU* 1.3 69.8 + - + +
97A GLN* 3.4 19.9 - - - +
98A TYR 3.6 11.2 - - - +
100A VAL* 4.4 10.3 - - + -
123A ALA* 3.4 37.9 - - + +
124A SER* 3.6 19.1 - - - +
125A PRO* 4.1 12.6 - - + +
128A LEU* 3.8 27.8 - - + -
131A PHE* 4.6 2.7 - - + -
134A ILE* 3.9 12.1 - - + -
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Residues in contact with LEU 94 (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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90A LYS* 2.9 53.2 + - + +
93A LEU* 1.3 79.7 - - + +
95A VAL* 1.3 67.9 + - + +
97A GLN* 4.6 5.0 - - - +
125A PRO* 6.5 0.4 - - + -
128A LEU* 4.6 7.2 - - + -
134A ILE* 4.2 22.7 - - + +
139A ASN* 3.6 45.3 - - + +
197A LYS* 5.8 7.6 - - - +
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Residues in contact with VAL 95 (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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91A ASP* 2.9 36.3 + - - +
93A LEU 3.3 0.4 - - - -
94A LEU* 1.3 84.9 - - + +
96A ARG* 1.3 66.9 + - - +
97A GLN* 2.7 25.3 + - - +
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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