Contacts of the helix formed by residues 53 - 62 (chain C) in PDB entry 5TF6
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 ASN 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER 3.4 4.4 + - - +
52C TYR* 1.3 74.6 - - - +
54C GLN* 1.3 71.0 + - - +
55C ASN* 3.6 27.6 + - - +
56C LYS* 3.0 35.6 + - - +
57C VAL* 3.2 21.3 + - - +
72C VAL* 4.1 6.1 - - - -
81C ARG* 3.9 9.6 - - - +
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Residues in contact with GLN 54 (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 ASN* 1.3 78.8 - - - +
55C ASN* 1.3 65.8 + - - +
57C VAL* 3.1 3.3 + - - +
58C TYR* 3.0 20.7 + - - +
69C HIS* 5.0 3.6 - - - -
70C VAL* 3.6 26.8 + - + +
71C ASP* 5.0 2.6 - - - +
72C VAL* 3.9 18.8 + - + +
506C GOL 3.3 42.7 + - - +
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN* 3.3 18.1 + - - +
54C GLN* 1.3 81.4 - - - +
56C LYS* 1.3 59.0 + - - +
58C TYR* 3.4 9.9 - - - +
59C LYS* 3.0 53.1 + - - +
506C GOL 5.1 3.1 - - - -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 3.4 29.2 + - - -
52C TYR* 3.7 39.7 - - + +
53C ASN* 3.0 27.0 + - - +
54C GLN 3.1 0.4 + - - -
55C ASN* 1.3 76.5 - - - +
57C VAL* 1.3 61.6 + - - +
59C LYS* 3.7 10.8 - - + +
60C TYR* 3.0 27.7 + - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.9 25.4 - - + -
52C TYR* 4.0 13.7 - - + -
53C ASN 3.2 13.4 + - - +
54C GLN 3.4 6.7 - - - +
56C LYS* 1.3 74.0 - - - +
58C TYR* 1.3 67.0 + - - +
60C TYR* 3.0 4.3 + - - -
61C PHE* 3.0 30.5 + - + +
70C VAL* 3.6 21.5 - - + -
72C VAL* 4.1 14.1 - - + -
83C ALA* 4.2 6.5 - - + -
85C ILE* 3.7 26.5 - - + -
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Residues in contact with TYR 58 (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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54C GLN 3.0 12.4 + - - +
55C ASN* 3.4 12.6 - - - +
57C VAL* 1.3 77.9 - - - +
59C LYS* 1.3 74.0 + - - +
62C LYS* 2.9 61.3 + - + +
67C ILE* 3.9 46.7 + - + +
70C VAL* 4.3 3.8 - - + +
506C GOL 3.9 37.7 - - - +
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Residues in contact with LYS 59 (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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78B G 5.2 12.1 - - - +
79B A 3.9 18.3 + - - +
55C ASN* 3.0 50.4 + - - +
56C LYS* 3.7 11.4 - - + +
57C VAL 3.2 0.2 - - - -
58C TYR* 1.3 86.7 - - - +
60C TYR* 1.3 64.0 + - - +
61C PHE 3.4 0.3 + - - -
62C LYS* 4.0 30.3 - - - +
63C HIS* 5.1 1.2 + - - -
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Residues in contact with TYR 60 (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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48C LEU* 6.1 0.9 - - + -
52C TYR* 3.9 23.8 - + + -
56C LYS 3.0 18.6 + - - +
57C VAL* 3.0 5.3 + - - +
59C LYS* 1.3 79.2 - - - +
61C PHE* 1.3 84.1 + + + +
63C HIS* 3.3 25.5 + + - -
99C LYS* 4.0 22.8 - - + +
102C LYS* 4.3 17.5 - - - +
103C VAL 4.4 3.6 + - - -
104C VAL* 3.5 33.0 - - + +
109C ILE* 4.8 3.8 - - + +
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Residues in contact with PHE 61 (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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45C VAL* 3.8 31.9 - - + -
48C LEU* 4.9 9.0 - - + -
57C VAL* 3.0 29.8 + - + +
60C TYR* 1.3 101.2 - + + +
62C LYS* 1.3 58.8 + - - +
63C HIS 3.2 3.4 - - - -
64C CYS* 3.0 43.7 + - - +
67C ILE* 3.9 9.4 - - + -
85C ILE* 3.6 22.4 - - + -
87C PHE* 4.0 7.6 - - + -
96C ALA* 4.2 23.6 - - + -
99C LYS* 3.9 18.4 - - + -
109C ILE* 4.3 14.8 - - + -
111C VAL* 4.4 5.6 - - + -
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Residues in contact with LYS 62 (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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78B G 3.5 28.3 + - - +
79B A 3.3 26.9 - - + +
58C TYR* 2.9 49.9 + - + +
59C LYS* 4.0 27.5 - - - +
60C TYR 3.7 0.4 - - - -
61C PHE* 1.3 76.6 - - - +
63C HIS* 1.3 58.4 + - - +
64C CYS 3.1 0.7 - - - -
65C GLY* 2.8 24.5 - - - +
66C PRO* 4.9 0.6 - - + +
67C ILE* 3.7 15.5 - - + +
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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