Contacts of the helix formed by residues 66 - 77 (chain D) in PDB entry 1YFL
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 SER 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D VAL* 1.3 78.1 - - - +
67D TRP* 1.3 54.2 + - - +
68D ASP* 2.7 31.3 + - - +
69D ASP* 2.7 39.7 + - - +
70D VAL* 3.6 2.4 + - - +
140D PHE* 3.6 7.9 - - - -
144D LYS* 5.6 0.4 - - - -
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Residues in contact with TRP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D SER* 1.3 71.0 - - - +
68D ASP* 1.3 66.0 + - - +
69D ASP 3.4 0.2 - - - -
70D VAL* 3.7 28.7 - - + -
71D LEU* 3.2 37.5 + - + +
104D TYR* 4.0 17.9 - - - -
108D PHE* 4.2 1.8 - + - -
132D ILE* 4.0 29.6 - - + -
133D ASN 5.7 0.4 - - - -
136D SER* 3.5 26.2 - - - -
137D GLU* 3.4 53.9 + - + +
140D PHE* 3.3 41.9 - + + -
141D ASN* 5.4 0.9 - - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D SER* 2.7 16.1 + - - +
67D TRP* 1.3 83.4 + - - +
69D ASP* 1.3 57.3 + - - +
70D VAL 3.1 1.8 - - - -
71D LEU* 3.0 15.3 + - - +
72D LYS* 2.8 35.5 + - - +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 6.3 0.4 - - - +
64D ASN 4.8 0.2 - - - +
65D VAL* 3.2 20.4 - - + +
66D SER* 2.7 39.0 + - - +
68D ASP* 1.3 79.5 - - - +
70D VAL* 1.3 61.3 + - - +
72D LYS* 3.9 7.4 - - - +
73D VAL* 3.2 29.3 + - + +
101D LEU* 4.6 9.9 - - + +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 4.6 6.3 - - + -
66D SER 4.0 10.3 - - - +
67D TRP* 3.7 44.2 - - + +
68D ASP 3.1 0.6 - - - -
69D ASP* 1.3 79.2 - - - +
71D LEU* 1.3 58.0 + - - +
73D VAL* 3.5 5.5 + - - +
74D ILE* 3.0 43.2 + - + +
101D LEU* 4.5 9.2 - - + -
104D TYR* 3.8 31.9 - - + -
105D VAL* 4.5 13.1 - - + +
108D PHE* 4.6 5.4 - - + -
140D PHE* 4.7 2.0 - - + -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TRP* 3.2 43.7 + - + +
68D ASP* 3.0 18.3 + - - +
70D VAL* 1.3 77.1 - - + +
72D LYS* 1.3 56.3 + - - +
74D ILE* 3.0 8.0 + - + +
75D LYS* 2.7 37.2 + - - +
132D ILE* 4.2 24.2 - - + -
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASP 2.8 18.9 + - - +
69D ASP* 3.9 10.1 - - - +
70D VAL 3.4 0.2 - - - -
71D LEU* 1.3 72.2 - - - +
73D VAL* 1.3 59.8 + - + +
75D LYS* 3.6 5.6 - - - +
76D GLN* 2.8 32.9 + - - +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ASP* 3.2 17.8 + - + +
70D VAL 3.8 4.0 - - - +
71D LEU 3.1 0.4 - - - -
72D LYS* 1.3 76.5 - - + +
74D ILE* 1.3 66.4 + - - +
76D GLN* 4.2 13.7 - - - +
77D TYR* 3.3 31.5 + - + +
79D LEU* 4.7 0.3 - - - +
90D LEU* 4.6 0.9 - - + -
101D LEU* 3.3 23.1 - - + -
102D LEU* 3.5 28.3 - - + -
105D VAL* 3.7 23.1 - - + -
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.0 24.7 + - + +
71D LEU* 3.0 12.3 + - + +
73D VAL* 1.3 73.8 - - - +
75D LYS* 1.3 68.7 + - - +
77D TYR* 3.2 3.5 + - - +
78D LYS 2.9 16.5 + - - -
79D LEU* 3.3 38.5 + - + +
105D VAL* 3.9 17.0 - - + -
109D HIS* 4.4 10.1 - - + +
131D THR* 5.0 1.1 - - - +
132D ILE* 3.3 48.5 - - + -
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU 2.7 20.6 + - - +
72D LYS* 3.6 7.9 - - - +
74D ILE* 1.3 72.0 - - - +
76D GLN* 1.3 56.3 + - - +
78D LYS* 2.5 31.0 + - - +
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LYS* 2.8 22.3 + - - +
73D VAL* 3.9 15.8 - - - +
74D ILE 3.4 0.2 - - - -
75D LYS* 1.3 72.4 - - - +
77D TYR* 1.3 84.2 + - + +
78D LYS* 3.8 0.7 + - - +
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Residues in contact with TYR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 3.3 24.8 + - + +
74D ILE 3.2 2.0 + - - -
75D LYS 2.7 1.8 + - - -
76D GLN* 1.3 104.9 + - + +
78D LYS* 1.3 75.1 + - - +
79D LEU* 3.3 17.2 + - + -
86D GLU* 3.3 23.0 - - + +
89D LYS* 4.2 17.5 - - + -
90D LEU* 3.5 47.3 - - + +
93D ASP* 2.7 40.0 + - - +
102D LEU* 4.2 10.2 - - + +
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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