Contacts of the helix formed by residues 69 - 78 (chain I) in PDB entry 1YI2
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 PRO 69 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11640 U 3.0 28.3 - - - +
67I VAL 3.6 0.4 - - - -
68I PRO* 1.3 92.9 - - + +
70I THR* 1.3 64.2 + - - +
71I ALA* 4.6 6.7 - - + +
72I GLU* 2.8 41.1 + - + +
73I LEU* 3.2 19.9 + - - +
107I LYS* 3.3 1.1 - - - -
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Residues in contact with THR 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11630 G 3.1 21.9 + - - +
11640 U 2.6 14.6 + - - -
69I PRO* 1.3 66.7 - - - +
71I ALA* 1.3 57.8 + - - +
72I GLU 2.7 16.2 + - - -
73I LEU* 2.9 12.8 + - - +
74I ILE* 3.0 36.8 + - + +
103I ILE* 5.1 1.1 - - + -
107I LYS* 2.8 32.9 + - - +
123I VAL* 4.4 20.3 - - + +
126I THR* 4.2 19.1 - - - +
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Residues in contact with ALA 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11640 U 4.6 0.4 + - - -
11660 A 4.2 2.9 - - - +
11670 G 3.0 43.1 - - - +
69I PRO* 4.6 4.7 - - + +
70I THR* 1.3 77.5 - - - +
72I GLU* 1.3 59.5 + - + +
74I ILE* 3.9 10.5 - - - +
75I LYS* 2.8 39.6 + - - +
126I THR* 4.9 8.2 - - + +
130I LEU* 5.4 4.7 - - + +
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Residues in contact with GLU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I PRO* 4.1 10.4 - - + +
69I PRO* 2.8 41.0 + - + +
70I THR 2.7 5.1 + - - -
71I ALA* 1.3 74.2 - - + +
73I LEU* 1.3 56.6 + - + +
74I ILE 2.9 4.3 - - - -
75I LYS* 2.7 34.3 + - + +
76I ASP* 2.8 17.5 + - - +
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I VAL* 4.7 2.0 - - + -
68I PRO* 4.1 25.8 - - + +
69I PRO 3.2 10.1 + - - +
70I THR 2.9 10.0 + - - +
72I GLU* 1.3 74.9 - - + +
74I ILE* 1.3 61.0 + - - +
76I ASP* 3.0 23.9 - - - +
77I GLU* 3.8 7.3 + - - +
103I ILE* 3.8 34.2 - - + +
106I GLN* 3.4 36.3 - - + +
107I LYS* 3.0 33.2 - - + +
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Residues in contact with ILE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I THR* 3.0 39.4 + - + +
71I ALA* 3.9 8.1 - - - +
72I GLU 2.8 1.0 + - - -
73I LEU* 1.3 74.9 - - - +
75I LYS* 1.3 55.0 - - + +
76I ASP 2.7 15.9 + - - -
77I GLU* 4.0 0.5 - - - +
78I ALA* 2.9 31.0 + - + +
95I LEU* 4.6 7.0 - - + +
103I ILE* 4.2 16.6 - - + -
123I VAL* 4.4 2.5 - - + +
126I THR* 3.5 25.1 - - - +
127I CYS* 3.6 18.6 - - - -
130I LEU* 4.7 5.8 - - + -
132I VAL* 4.1 32.8 - - + -
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Residues in contact with LYS 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11670 G 3.8 15.6 + - - -
11680 C 3.4 31.6 + - - -
71I ALA* 2.8 32.4 + - - +
72I GLU* 2.7 20.5 + - + +
74I ILE* 1.3 76.0 - - + +
76I ASP* 1.3 62.8 + - - +
78I ALA* 4.3 3.6 - - - -
79I GLY 3.8 3.6 + - - -
80I PHE 2.6 30.5 + - - +
81I GLU* 3.0 28.3 + - - +
82I THR 5.7 0.7 - - - -
83I GLY* 4.8 5.4 - - - +
130I LEU* 5.7 5.6 - - + -
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Residues in contact with ASP 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I GLU* 2.8 20.3 - - - +
73I LEU* 3.0 25.5 - - - +
74I ILE 2.7 6.5 + - - -
75I LYS* 1.3 73.8 - - - +
77I GLU* 1.3 59.2 + - + +
78I ALA 2.9 3.1 - - - -
79I GLY* 2.6 29.1 + - - -
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I LEU 3.8 7.6 + - - +
74I ILE 3.5 1.8 + - - -
76I ASP* 1.3 79.7 - - + +
78I ALA* 1.3 60.1 + - - +
79I GLY* 4.5 0.2 - - - -
94I ASP 5.0 0.3 - - - +
95I LEU* 4.4 13.5 - - + -
99I GLN* 3.2 42.9 - - + +
102I GLN* 3.6 28.6 + - - +
103I ILE* 3.3 19.8 - - + +
106I GLN* 5.1 4.4 + - - -
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Residues in contact with ALA 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ILE* 2.9 31.5 + - + +
75I LYS* 4.4 2.7 - - - -
76I ASP 2.8 0.6 + - - -
77I GLU* 1.3 77.8 - - - +
79I GLY* 1.3 58.3 + - - +
80I PHE* 2.9 32.8 - - + +
93I ALA* 3.9 22.7 - - + +
94I ASP 4.5 12.0 - - - +
95I LEU* 4.5 3.8 - - + +
132I VAL* 5.1 0.4 - - + -
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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