Contacts of the helix formed by residues 62 - 74 (chain B) in PDB entry 1TU8
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 GLN 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A MET* 3.5 21.1 - - + +
92A GLU* 3.4 28.3 - - + +
93A GLY* 3.5 19.6 - - - -
96A ASP* 2.8 23.4 + - - -
47B PHE* 3.6 21.1 - - + +
49B GLN* 5.9 0.4 - - - +
51B PRO 3.8 5.3 + - - -
61B VAL* 1.3 81.3 - - - +
63B SER* 1.3 67.2 + - - +
64B GLY 3.3 1.1 - - - -
65B ALA* 3.0 10.3 + - + -
66B ILE* 2.9 21.9 + - - +
95B ARG* 5.0 0.2 + - - -
2002B GTX 2.9 35.1 + - - -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.9 22.7 + - - +
17B ILE* 3.9 15.9 - - - +
51B PRO* 3.9 14.8 - - - +
62B GLN* 1.3 71.1 - - - +
64B GLY* 1.3 55.3 + - - +
66B ILE* 3.3 6.2 + - - +
67B LEU* 3.0 31.0 + - - +
95B ARG* 2.9 21.7 + - - -
2002B GTX 2.5 36.2 + - - -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 4.6 3.2 + - - -
62B GLN* 3.3 0.8 + - - -
63B SER* 1.3 82.2 + - - +
65B ALA* 1.3 56.9 + - - +
67B LEU* 3.5 7.5 + - - +
68B ARG* 3.1 57.2 + - - +
95B ARG* 3.5 19.2 - - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 4.4 4.8 - - - +
88A ASP* 3.6 21.8 - - + +
89A MET* 3.6 36.6 - - + +
92A GLU* 4.6 1.0 - - + +
60B ILE* 4.5 5.2 - - + -
61B VAL 4.0 5.2 - - - +
62B GLN* 3.0 12.4 + - + +
64B GLY* 1.3 72.5 - - - +
66B ILE* 1.3 66.9 + - - +
68B ARG* 3.6 3.3 - - - +
69B HIS* 3.0 25.7 + - - +
72B ARG* 5.0 1.2 + - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.7 0.9 - - + -
17B ILE* 3.7 36.8 - - + -
51B PRO* 3.8 24.0 - - + +
52B CYS 4.2 0.4 - - - -
53B LEU* 3.7 34.5 - - + +
60B ILE* 3.5 38.8 - - + +
62B GLN 2.9 23.0 + - - +
63B SER* 3.5 7.0 - - - +
65B ALA* 1.3 74.5 - - - +
67B LEU* 1.3 64.4 + - - +
69B HIS* 3.2 5.3 + - - +
70B LEU* 3.0 25.6 + - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 4.3 22.9 - - + +
17B ILE* 4.0 22.4 - - + -
20B PHE* 3.9 35.2 - - + -
63B SER* 3.0 15.6 + - - +
64B GLY* 3.8 8.7 - - - +
66B ILE* 1.3 77.8 - - - +
68B ARG* 1.3 57.8 + - - +
70B LEU* 3.4 6.4 + - + +
71B ALA* 2.9 29.7 + - - +
91B CYS* 4.5 14.4 - - - -
95B ARG* 6.2 1.8 - - - +
149B TYR* 4.0 35.4 - - + +
152B TYR* 5.6 0.2 - - + -
153B ALA* 4.8 1.8 - - + -
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.6 39.2 - - - +
88A ASP* 2.7 44.4 + - - +
92A GLU* 3.6 21.4 - - - -
64B GLY* 3.1 39.6 + - - +
65B ALA 4.1 0.2 - - - +
67B LEU* 1.3 74.2 - - - +
69B HIS* 1.3 60.8 + - - +
71B ALA* 3.5 6.3 - - - +
72B ARG* 3.0 47.7 + - - +
77B ASN* 5.0 5.2 - - - +
88B ASP* 4.0 7.4 + - - -
91B CYS* 6.0 3.0 - - - +
92B GLU* 3.8 11.5 + - - -
95B ARG* 5.5 0.8 - - - +
149B TYR* 3.7 34.7 + - + +
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 2.8 34.3 - - + +
85A THR* 3.3 21.5 - - + +
53B LEU* 4.3 10.9 - - + +
55B ASP* 2.7 32.4 + - + -
58B GLN* 6.4 0.4 - - - +
60B ILE* 3.5 27.0 - - + +
65B ALA 3.0 18.6 + - - +
66B ILE* 3.5 4.0 - - - +
68B ARG* 1.3 74.8 - - - +
70B LEU* 1.3 68.3 + - + +
72B ARG* 3.3 13.9 + - - +
73B LYS* 3.1 37.1 + - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 4.0 23.1 - - + +
17B ILE* 4.0 26.5 - - + -
20B PHE* 3.7 25.1 - - + -
21B LEU* 4.1 25.6 - - + -
26B ILE* 5.2 3.4 - - + -
53B LEU* 4.0 21.8 - - + -
66B ILE* 3.0 25.3 + - + +
67B LEU* 3.8 6.1 - - + +
69B HIS* 1.3 81.0 - - + +
71B ALA* 1.3 57.6 + - - +
73B LYS* 3.2 7.0 + - + +
74B TYR* 2.9 36.3 + - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.8 9.8 - - - -
67B LEU 2.9 19.1 + - - +
68B ARG* 3.5 6.3 - - - +
69B HIS 3.2 0.2 - - - -
70B LEU* 1.3 77.7 - - - +
72B ARG* 1.3 57.0 + - - +
75B ASN* 2.9 11.8 + - - -
76B LEU* 2.8 35.8 + - - +
77B ASN* 3.6 8.3 + - + +
149B TYR* 3.4 32.1 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.0 40.7 + - - +
84A THR* 3.7 23.6 + - - +
85A THR* 3.3 28.3 + - - +
88A ASP* 4.8 6.7 + - - +
65B ALA 5.0 0.4 + - - -
68B ARG* 3.0 34.1 + - - +
69B HIS* 3.3 16.9 + - - +
71B ALA* 1.3 77.2 - - - +
73B LYS* 1.3 63.3 + - - +
74B TYR 3.4 0.5 + - - -
75B ASN* 3.5 7.5 + - - +
77B ASN* 3.7 26.1 + - + +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 5.1 9.2 - - + -
3B TYR* 2.9 26.5 + - + +
55B ASP* 2.6 31.7 + - - +
69B HIS* 3.1 39.8 + - + +
70B LEU* 3.2 9.8 + - + +
72B ARG* 1.3 77.9 - - - +
74B TYR* 1.3 71.6 + - + +
75B ASN 3.8 0.7 + - - -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 3.7 25.3 + + - -
20B PHE* 4.2 13.9 - + + -
24B GLN* 4.9 13.6 - - - +
26B ILE* 3.4 47.5 - - + +
70B LEU* 2.9 20.1 + - + +
73B LYS* 1.3 87.4 - - + +
75B ASN* 1.3 71.2 - - - +
76B LEU* 3.2 18.0 - - + +
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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