Contacts of the helix formed by residues 58 - 73 (chain Y) in PDB entry 1T6B
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 58 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55Y VAL 2.9 10.3 + - - +
57Y ASN* 1.3 95.1 + - - +
59Y TRP* 1.3 65.4 + - - +
60Y ILE* 3.0 3.6 - - - +
61Y GLU* 2.6 50.8 + - - +
62Y ILE* 3.1 14.2 + - - +
178Y VAL* 4.0 12.1 - - + -
179Y LEU* 3.5 38.6 - - + +
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Residues in contact with TRP 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 3.9 22.4 - - + -
50Y ASP 3.3 27.6 - - - -
51Y LYS* 3.9 8.1 - - + -
55Y VAL* 3.3 5.8 + - + -
56Y ALA 3.5 6.3 + - - +
57Y ASN 3.7 0.4 - - - -
58Y ASN* 1.3 76.7 - - - +
60Y ILE* 1.3 60.5 + - + +
62Y ILE* 3.1 26.8 + - + +
63Y TYR* 2.7 44.4 + - + +
84Y VAL* 4.1 12.3 - - + -
109Y LEU* 2.9 38.4 + - + -
110Y LYS* 4.7 6.0 - - - +
112Y VAL* 3.6 38.6 - - + +
114Y PRO* 3.5 31.0 - - + -
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Residues in contact with ILE 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y ALA 6.1 0.9 - - - +
57Y ASN 5.4 4.2 - - - +
58Y ASN* 3.0 1.9 - - - -
59Y TRP* 1.3 85.7 - - + +
61Y GLU* 1.3 62.5 + - + +
63Y TYR* 3.9 7.4 - - + +
64Y ASN* 3.1 41.3 + - - +
110Y LYS* 5.6 11.0 - - - -
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Residues in contact with GLU 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Y ASN* 2.6 44.9 + - + +
60Y ILE* 1.3 78.1 - - - +
62Y ILE* 1.3 63.8 + - + +
64Y ASN* 3.9 5.7 - - - +
65Y PHE* 3.1 23.4 + - - +
178Y VAL* 3.6 13.0 - - - +
179Y LEU 4.7 1.9 + - - -
199Y VAL* 3.9 30.0 - - + +
200Y LYS* 4.8 13.7 - - - +
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Residues in contact with ILE 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 4.3 13.9 - - + -
50Y ASP 3.9 19.5 - - - +
55Y VAL* 4.0 16.4 - - + -
58Y ASN 3.1 15.7 + - - +
59Y TRP* 3.1 35.3 + - + +
61Y GLU* 1.3 77.3 - - + +
63Y TYR* 1.3 68.6 + - - +
65Y PHE* 3.2 7.7 + - - +
66Y VAL* 3.0 21.5 + - - +
146Y LEU* 4.2 26.0 - - + +
178Y VAL* 3.9 34.1 - - + -
199Y VAL* 5.4 0.4 - - + -
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Residues in contact with TYR 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Y TRP* 2.7 37.0 + - + +
60Y ILE* 4.0 8.7 - - + +
61Y GLU 3.4 0.2 - - - -
62Y ILE* 1.3 73.2 - - - +
64Y ASN* 1.3 63.4 + - - +
66Y VAL* 2.8 12.8 + - - +
67Y GLN* 2.8 64.4 + - + +
106Y LEU* 3.4 48.9 + - + +
107Y GLU* 4.7 5.5 + - - -
109Y LEU* 3.9 21.8 - - + -
110Y LYS* 3.7 40.2 - - + +
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Residues in contact with ASN 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Y ILE* 3.1 32.8 + - - +
61Y GLU* 3.9 6.6 - - - +
63Y TYR* 1.3 96.3 - - - +
65Y PHE* 1.3 64.7 + - - +
67Y GLN* 3.8 10.7 + - - +
68Y GLN* 2.9 30.8 + - - +
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Residues in contact with PHE 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y PHE* 4.7 1.3 - + - -
61Y GLU 3.1 17.4 + - - +
62Y ILE* 3.5 5.4 - - - +
63Y TYR 3.1 0.2 - - - -
64Y ASN* 1.3 79.8 - - - +
66Y VAL* 1.3 66.2 + - - +
68Y GLN* 3.3 10.2 + - - +
69Y LEU* 3.1 42.1 + - + +
144Y ILE* 4.5 2.0 - - + -
146Y LEU* 3.9 29.8 - - + -
176Y VAL* 4.0 21.1 - - + -
199Y VAL* 4.0 25.4 - - + -
202Y GLY 3.9 6.7 - - - -
203Y PHE* 3.7 36.3 - + + -
206Y LEU* 3.7 23.1 - - + -
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Residues in contact with VAL 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y PHE* 3.9 27.8 - - + -
49Y LEU* 3.6 32.8 - - + -
62Y ILE 3.0 12.8 + - - +
63Y TYR* 2.8 8.9 + - - +
65Y PHE* 1.3 79.3 - - + +
67Y GLN* 1.3 62.7 + - - +
68Y GLN 3.2 0.2 + - - -
69Y LEU* 3.2 3.6 + - - +
70Y ALA* 2.9 20.1 + - - +
82Y PHE* 3.6 32.5 - - + -
106Y LEU* 3.9 4.5 - - + -
109Y LEU* 3.8 17.3 - - + -
146Y LEU* 5.2 0.2 - - + -
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Residues in contact with GLN 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Y TYR* 2.8 53.3 + - + +
64Y ASN* 3.8 14.1 + - - +
66Y VAL* 1.3 72.2 - - - +
68Y GLN* 1.3 59.5 + - - +
70Y ALA* 3.1 3.8 + - - +
71Y GLU* 2.9 56.6 + - + +
106Y LEU* 4.1 23.0 - - + +
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Residues in contact with GLN 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Y ASN* 2.9 20.6 + - - +
65Y PHE* 4.0 11.1 - - - +
67Y GLN* 1.3 79.1 - - + +
69Y LEU* 1.3 59.1 + - - +
71Y GLU* 3.5 12.9 + - - +
72Y ARG* 3.3 16.1 + - - +
203Y PHE* 3.5 61.5 - - + +
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Residues in contact with LEU 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU* 4.9 1.5 - - + +
47Y PHE* 3.6 38.1 - - + -
65Y PHE* 3.1 21.4 + - + +
66Y VAL 3.7 3.6 - - - +
68Y GLN* 1.3 73.6 - - - +
70Y ALA* 1.3 64.5 + - - +
71Y GLU 3.1 1.6 - - - -
72Y ARG* 3.2 2.9 + - + +
73Y PHE* 3.1 56.1 + - + +
144Y ILE* 3.8 7.0 - - + -
203Y PHE* 3.4 32.5 - - + +
206Y LEU* 3.4 34.1 - - + -
207Y LYS* 5.3 2.7 - - + -
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Residues in contact with ALA 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y PHE* 5.1 1.8 - - - -
66Y VAL 2.9 15.9 + - - +
67Y GLN* 3.1 8.9 + - - +
69Y LEU* 1.3 71.7 - - - +
71Y GLU* 1.3 61.5 + - + +
73Y PHE 3.9 4.4 - - - +
74Y VAL* 3.6 5.0 - - - +
80Y LEU* 4.0 28.3 - - + -
82Y PHE* 4.7 2.2 - - + -
99Y ARG* 2.9 26.6 + - - +
102Y ILE* 4.3 6.5 - - + -
106Y LEU* 4.0 25.1 - - + -
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Residues in contact with GLU 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Y GLN* 2.9 48.2 + - + +
68Y GLN* 3.9 14.0 - - - +
69Y LEU 3.1 0.6 - - - -
70Y ALA* 1.3 76.7 - - + +
72Y ARG* 1.3 64.5 + - - +
74Y VAL* 3.5 18.3 - - + +
99Y ARG* 5.0 0.9 - - - +
106Y LEU* 6.1 2.0 - - + -
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Residues in contact with ARG 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Y GLN 3.3 13.6 + - - +
69Y LEU* 3.2 5.9 + - - +
71Y GLU* 1.3 81.1 - - - +
73Y PHE* 1.3 88.2 + - + +
74Y VAL* 3.2 7.4 + - - +
203Y PHE* 4.2 15.9 - - + -
207Y LYS* 3.5 50.1 - - + +
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Residues in contact with PHE 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU* 3.8 22.7 - - + -
69Y LEU* 3.1 40.6 + - + +
70Y ALA 3.9 3.5 - - - +
71Y GLU 3.6 0.4 - - - -
72Y ARG* 1.3 102.5 - - + +
74Y VAL* 1.3 58.8 + - - +
75Y SER* 3.5 3.1 + - - -
78Y MET* 3.4 38.6 - - + +
80Y LEU* 4.2 16.0 - - + +
99Y ARG* 3.2 15.7 + - - -
207Y LYS* 4.1 17.9 - - + -
210Y ILE* 4.1 43.1 - - + -
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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