Contacts of the helix formed by residues 62 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.5 21.6 - - + +
51A PRO 3.8 6.3 + - - -
61A VAL* 1.3 81.4 - - + +
63A SER* 1.3 66.5 + - - +
64A GLY 3.2 1.3 - - - -
65A ALA* 3.0 9.2 + - + -
66A ILE* 2.9 22.8 + - - +
2001A GTX 3.0 41.5 + - - -
89B MET* 3.6 20.0 - - + +
92B GLU* 3.5 31.4 + - + +
93B GLY* 3.5 13.9 + - - -
96B ASP* 2.8 20.4 + - - +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.9 23.9 - - - +
17A ILE* 3.8 14.5 - - - +
51A PRO* 3.8 16.7 - - - +
62A GLN* 1.3 71.2 - - - +
64A GLY* 1.3 55.8 + - - +
66A ILE* 3.5 6.9 + - - +
67A LEU* 3.1 28.2 + - - +
95A ARG* 2.9 20.4 + - - -
2001A GTX 2.6 35.7 + - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 3.2 1.2 - - - +
63A SER* 1.3 79.9 + - - +
65A ALA* 1.3 60.5 + - - +
67A LEU* 3.5 4.1 + - - +
68A ARG* 3.0 56.1 + - - +
95A ARG* 3.3 19.5 - - - +
2001A GTX 4.5 0.4 + - - -
92B GLU* 4.7 3.4 + - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 4.6 4.5 - - + -
61A VAL 4.0 5.8 - - - +
62A GLN* 3.0 13.2 + - + +
64A GLY* 1.3 72.6 - - - +
66A ILE* 1.3 64.7 + - - +
68A ARG* 3.6 4.0 - - - +
69A HIS* 3.0 26.0 + - - +
72A ARG* 4.9 0.9 + - - -
85B THR* 4.4 5.3 - - + +
88B ASP* 3.5 21.1 - - + +
89B MET* 3.6 37.5 - - + +
92B GLU* 4.6 1.2 - - + +
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Residues in contact with ILE 66 (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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5A LEU* 4.9 0.7 - - + -
17A ILE* 3.7 28.5 - - + -
51A PRO* 3.8 27.6 - - + +
52A CYS 4.3 0.2 - - - -
53A LEU* 3.8 34.1 - - + +
60A ILE* 3.3 40.4 - - + +
61A VAL 4.0 0.2 - - - -
62A GLN 2.9 23.3 + - - +
63A SER* 3.6 10.5 - - - +
65A ALA* 1.3 76.1 - - - +
67A LEU* 1.3 62.5 + - - +
69A HIS* 3.3 4.6 + - - +
70A LEU* 3.1 23.7 + - + +
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Residues in contact with LEU 67 (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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16A PRO* 4.1 25.1 - - + +
17A ILE* 4.2 15.5 - - + -
20A PHE* 3.9 36.1 - - + -
63A SER 3.1 17.8 + - - +
64A GLY* 4.1 4.7 - - - +
66A ILE* 1.3 79.3 - - - +
68A ARG* 1.3 57.5 - - - +
70A LEU* 3.4 6.5 + - + +
71A ALA* 3.0 27.9 + - - +
91A CYS* 4.5 11.4 - - - -
149A TYR* 3.6 39.0 - - + +
153A ALA* 4.7 2.5 - - + +
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Residues in contact with ARG 68 (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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64A GLY* 3.0 39.5 + - - +
65A ALA 4.0 0.4 - - - +
67A LEU* 1.3 78.3 - - - +
69A HIS* 1.3 60.9 + - - +
71A ALA* 3.4 7.7 + - - +
72A ARG* 3.1 40.2 + - - +
77A ASN* 5.0 3.3 + - - +
88A ASP* 4.1 6.7 + - - -
91A CYS* 6.0 3.4 - - - +
92A GLU* 3.5 20.0 + - - -
95A ARG* 5.4 1.2 - - - +
149A TYR* 3.9 32.5 + - + +
68B ARG* 3.6 31.0 - - - +
88B ASP* 2.7 45.5 + - - +
92B GLU* 3.5 24.2 + - - -
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Residues in contact with HIS 69 (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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53A LEU* 4.5 11.9 - - + -
55A ASP* 2.7 29.6 + - - -
58A GLN* 4.4 9.8 + - - -
60A ILE* 3.3 26.4 - - + +
65A ALA 3.0 18.4 + - - +
66A ILE* 3.7 3.1 - - - +
68A ARG* 1.3 73.2 - - - +
70A LEU* 1.3 68.6 + - + +
72A ARG* 3.2 13.1 + - - +
73A LYS* 3.0 41.5 + - + +
81B GLU* 2.6 32.8 + - + -
85B THR* 3.6 21.2 + - + +
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Residues in contact with LEU 70 (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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3A TYR* 4.2 18.6 - - + -
17A ILE* 3.9 27.8 - - + -
20A PHE* 3.7 23.1 - - + -
21A LEU* 4.0 22.9 - - + -
53A LEU* 3.9 22.0 - - + -
66A ILE* 3.1 25.0 + - + +
67A LEU* 3.7 7.6 - - + +
69A HIS* 1.3 80.4 - - + +
71A ALA* 1.3 63.7 + - - +
73A LYS* 3.2 4.6 + - + -
74A TYR* 3.0 41.4 + - + +
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Residues in contact with ALA 71 (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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20A PHE* 3.9 10.9 - - - -
67A LEU 3.0 15.6 + - - +
68A ARG 3.5 6.1 - - - +
69A HIS 3.3 0.2 - - - -
70A LEU* 1.3 77.6 - - - +
72A ARG* 1.3 62.1 + - - +
75A ASN* 3.0 5.2 + - - -
76A LEU 2.9 34.6 + - - +
77A ASN* 3.6 7.3 + - + +
149A TYR* 3.2 39.3 - - + -
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Residues in contact with ARG 72 (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 ALA 4.9 1.4 + - - -
68A ARG* 3.1 35.5 + - - +
69A HIS* 3.2 16.6 + - - +
71A ALA* 1.3 77.2 - - - +
73A LYS* 1.3 64.3 + - - +
74A TYR 3.3 0.7 + - - -
75A ASN* 3.4 8.2 + - - +
77A ASN* 3.6 24.9 + - - +
81B GLU* 2.9 31.4 + - - +
84B THR* 3.5 32.5 + - - +
85B THR* 3.1 32.9 + - - +
88B ASP* 4.7 5.7 + - - +
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Residues in contact with LYS 73 (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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3A TYR* 2.4 29.8 + - - +
55A ASP* 2.8 29.1 + - - +
58A GLN* 5.9 0.9 - - - -
69A HIS* 3.0 37.8 + - + +
70A LEU* 3.2 5.8 + - + +
72A ARG* 1.3 77.6 - - - +
74A TYR* 1.3 76.9 + - + +
75A ASN 4.0 0.2 + - - -
81B GLU* 5.5 4.0 - - + +
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Residues in contact with TYR 74 (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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3A TYR* 2.6 41.8 + + - -
20A PHE* 4.2 13.9 - + + -
24A GLN* 5.3 6.2 - - + +
26A ILE* 3.6 39.1 - - + +
70A LEU* 3.0 29.0 + - + +
73A LYS* 1.3 94.6 - - + +
75A ASN* 1.3 70.5 + - - +
76A LEU* 3.3 15.2 + - + +
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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