Contacts of the helix formed by residues 62 - 74 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.6 21.0 - - + +
51C PRO 3.8 6.7 + - - -
61C VAL* 1.3 81.6 - - + +
63C SER* 1.3 66.8 + - - +
64C GLY 3.1 1.5 - - - +
65C ALA* 3.0 9.6 + - + -
66C ILE* 2.9 22.6 + - - +
2004C GTX 2.9 42.9 + - - -
89D MET* 3.6 12.6 - - + +
92D GLU* 3.5 37.7 + - + +
93D GLY* 3.4 15.2 + - - -
96D ASP* 2.9 19.4 + - - +
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.9 24.0 - - - +
17C ILE* 3.8 8.2 - - - +
51C PRO* 3.7 27.3 - - - +
62C GLN* 1.3 70.3 - - - +
64C GLY* 1.3 55.7 + - - +
66C ILE* 3.5 8.0 + - - +
67C LEU* 3.1 29.6 + - - +
95C ARG* 2.9 21.1 + - - -
2004C GTX 2.7 30.7 + - - -
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Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLN* 3.1 1.6 + - - +
63C SER* 1.3 80.5 + - - +
65C ALA* 1.3 58.2 + - - +
67C LEU* 3.5 4.6 + - - +
68C ARG* 3.1 55.9 + - - +
95C ARG* 3.4 18.8 - - - +
2004C GTX 4.5 0.6 + - - -
92D GLU* 4.7 4.4 + - - -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 4.6 4.3 - - + -
61C VAL 4.0 6.1 - - - +
62C GLN* 3.0 13.2 + - + +
64C GLY* 1.3 72.6 - - - +
66C ILE* 1.3 60.4 + - - +
68C ARG* 3.6 3.4 - - - +
69C HIS* 2.9 31.4 + - - +
72C ARG* 4.9 0.9 + - - -
85D THR* 4.3 5.7 - - + +
88D ASP* 3.5 21.2 - - + +
89D MET* 3.7 36.6 - - + +
92D GLU* 4.5 0.8 - - + +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.9 1.1 - - + -
17C ILE* 3.7 26.2 - - + -
51C PRO* 3.8 26.9 - - + +
52C CYS 4.2 0.2 - - - -
53C LEU* 3.7 37.9 - - + +
60C ILE* 3.4 38.8 - - + +
61C VAL 4.0 0.4 - - - +
62C GLN 2.9 23.1 + - - +
63C SER* 3.6 10.5 - - - +
65C ALA* 1.3 76.1 - - - +
67C LEU* 1.3 62.0 + - - +
69C HIS* 3.6 4.8 + - - +
70C LEU* 3.0 24.4 + - + +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 4.3 20.0 - - + +
17C ILE* 4.3 18.4 - - + -
20C PHE* 3.8 37.2 - - + -
63C SER 3.1 17.1 + - - +
64C GLY* 4.1 4.5 - - - +
65C ALA 3.3 0.2 - - - -
66C ILE* 1.3 78.1 - - - +
68C ARG* 1.3 57.8 + - - +
70C LEU* 3.4 4.9 + - + +
71C ALA* 2.9 29.1 + - - +
91C CYS* 4.4 12.3 - - - -
149C TYR* 3.7 37.7 - - + +
153C ALA* 4.8 2.0 - - + -
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLY* 3.1 39.9 + - - +
65C ALA 4.0 0.2 - - - +
66C ILE 3.3 0.2 - - - -
67C LEU* 1.3 76.9 - - - +
69C HIS* 1.3 62.5 + - - +
71C ALA* 3.3 7.5 + - - +
72C ARG* 3.1 40.8 + - - +
77C ASN* 5.1 3.6 + - - +
88C ASP* 4.1 7.1 + - - -
91C CYS* 6.0 3.6 - - - +
92C GLU* 3.5 20.8 + - - -
95C ARG* 5.4 1.0 - - - +
149C TYR* 3.9 31.1 + - + +
68D ARG* 3.6 31.3 - - - +
88D ASP* 2.8 45.3 + - - +
92D GLU* 3.6 22.4 + - - -
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Residues in contact with HIS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 4.5 8.5 - - + +
55C ASP* 2.9 31.5 + - + -
58C GLN* 4.4 8.7 + - - -
60C ILE* 3.1 30.3 - - + +
65C ALA 2.9 18.4 + - - +
66C ILE* 3.6 4.0 + - - +
68C ARG* 1.3 72.5 - - - +
70C LEU* 1.3 67.8 + - + +
72C ARG* 3.2 13.2 + - - +
73C LYS* 3.1 31.4 + - + +
81D GLU* 2.7 36.5 - - + +
85D THR* 3.4 20.4 - - + +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TYR* 4.2 10.5 - - + +
17C ILE* 4.0 23.1 - - + -
20C PHE* 3.6 21.7 - - + -
21C LEU* 3.9 32.5 - - + -
53C LEU* 4.1 21.1 - - + -
55C ASP* 5.2 0.9 - - - +
66C ILE* 3.0 26.3 + - + +
67C LEU* 3.7 7.6 - - + +
69C HIS* 1.3 79.4 - - + +
71C ALA* 1.3 61.0 + - - +
73C LYS* 3.3 4.4 + - + -
74C TYR* 3.0 48.8 + - + +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.9 11.1 - - - -
67C LEU 2.9 15.4 + - - +
68C ARG 3.4 6.5 - - - +
69C HIS 3.2 0.2 - - - -
70C LEU* 1.3 77.0 - - - +
72C ARG* 1.3 61.7 + - - +
75C ASN* 3.0 3.8 + - - -
76C LEU 2.8 34.7 + - - +
77C ASN* 3.6 8.2 + - + +
149C TYR* 3.3 40.2 - - + -
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ALA 4.9 0.8 + - - -
68C ARG* 3.1 33.8 + - - +
69C HIS* 3.2 14.8 + - - +
71C ALA* 1.3 75.5 - - - +
73C LYS* 1.3 65.5 + - - +
74C TYR 3.3 0.7 + - - -
75C ASN* 3.3 11.5 + - - +
77C ASN* 3.7 25.3 + - - +
77D ASN* 5.9 0.2 - - - -
81D GLU* 3.0 44.4 + - - +
84D THR* 3.5 32.5 + - - +
85D THR* 3.1 21.6 + - - +
88D ASP* 4.7 6.1 + - - +
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TYR* 2.8 24.4 + - + +
55C ASP* 2.8 39.7 + - - +
69C HIS* 3.1 27.9 + - + +
70C LEU* 3.8 5.6 - - + +
72C ARG* 1.3 79.1 - - - +
74C TYR* 1.3 73.6 + - + +
75C ASN* 3.9 0.3 + - - +
81D GLU* 5.6 4.9 - - + -
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Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TYR* 2.7 39.7 + + - -
20C PHE* 4.2 15.5 - + + -
24C GLN* 5.4 6.6 - - + +
26C ILE* 3.6 39.7 - - + +
70C LEU* 3.0 31.8 + - + +
73C LYS* 1.3 93.5 - - + +
75C ASN* 1.3 70.1 + - - +
76C LEU* 3.3 15.0 + - + +
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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