Contacts of the helix formed by residues 63 - 75 (chain B) in PDB entry 1YYO
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 ARG 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A HIS* 6.2 1.6 - - - -
37A GLU* 3.4 20.8 + - - +
38A THR* 5.2 0.2 - - - -
61B ASN* 2.9 29.4 + - - +
62B LYS* 1.3 78.9 - - - +
64B GLU* 1.3 56.4 + - - +
65B GLY* 3.2 3.6 - - - +
66B PHE* 2.7 31.3 + - + +
67B LEU* 3.0 9.3 + - - -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 2.7 30.8 + - + +
38A THR* 6.0 0.2 - - - +
40A GLU* 5.9 4.7 - - + +
41A PHE* 4.1 25.1 - - + -
62B LYS 3.6 3.0 + - - -
63B ARG* 1.3 70.7 - - - +
65B GLY* 1.3 63.6 + - - +
66B PHE 2.9 0.5 + - - -
67B LEU* 3.0 1.5 + - - +
68B SER* 2.6 62.7 + - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 4.2 1.8 + - - -
63B ARG* 3.1 3.2 + - - +
64B GLU* 1.3 90.3 + - - +
66B PHE* 1.3 56.2 + - - +
68B SER* 5.1 0.2 - - - -
69B PRO* 3.3 18.4 - - - +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 3.6 15.9 - - - -
60B PRO* 4.0 15.9 - - + -
61B ASN* 3.1 56.5 - - + +
63B ARG* 2.7 19.4 + - + +
65B GLY* 1.3 74.5 - - - +
67B LEU* 1.3 58.9 + - - +
69B PRO* 3.2 16.6 - - + +
70B LEU* 3.6 27.8 - - + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 4.6 2.9 - - + -
41A PHE* 3.4 36.6 - - + -
55B LEU* 3.4 33.7 - - + +
56B VAL* 3.9 22.7 - - + -
59B SER* 3.5 7.4 - - - +
61B ASN 3.3 23.6 - - - +
62B LYS* 3.5 22.4 - - + +
63B ARG 3.0 11.9 + - - +
64B GLU 3.0 2.8 + - - +
66B PHE* 1.3 78.1 - - + +
68B SER* 1.3 66.5 + - - +
70B LEU* 3.0 6.9 + - - +
71B LYS* 2.8 23.2 + - - +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.8 13.0 - - - -
64B GLU* 2.6 44.6 + - - +
65B GLY* 5.1 0.4 - - - -
67B LEU* 1.3 71.7 - - - +
69B PRO* 1.3 69.3 - - - +
71B LYS* 3.1 7.5 + - - +
72B ALA* 2.9 24.0 + - - +
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY* 3.3 23.3 - - - +
66B PHE* 3.2 20.9 - - + +
67B LEU 3.4 0.4 - - - -
68B SER* 1.3 95.5 - - - +
70B LEU* 1.3 62.6 + - + +
72B ALA* 3.4 17.2 - - + +
73B TYR* 3.6 3.5 + - - +
148B VAL* 4.4 24.5 - - + +
149B LYS 4.6 1.4 + - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.0 26.5 - - + -
59B SER* 4.2 3.4 - - - +
60B PRO* 5.7 0.2 - - + -
66B PHE* 3.6 40.6 - - + +
67B LEU* 3.0 7.4 + - - +
69B PRO* 1.3 74.0 - - + +
71B LYS* 1.3 66.9 + - - +
73B TYR* 2.9 16.5 + - - +
74B LEU* 3.0 20.1 + - + +
142B ALA 5.3 0.2 - - - +
143B ILE* 4.3 20.0 - - + +
146B GLY* 4.0 21.5 - - - -
147B ARG 3.6 20.8 - - - +
148B VAL* 4.1 7.0 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.7 22.6 - - + -
44A ASP* 5.3 6.3 + - - -
48B ASN* 4.7 8.2 + - - +
51B ILE* 5.5 0.9 - - + -
52B VAL* 3.7 31.4 - - + +
55B LEU* 3.7 15.1 - - + +
67B LEU 2.8 15.4 + - - +
68B SER* 3.5 9.0 - - - +
70B LEU* 1.3 73.2 - - - +
72B ALA* 1.3 64.7 + - - +
74B LEU* 4.2 6.1 - - + -
75B ILE* 2.9 57.0 + - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B SER 2.9 11.8 + - - +
69B PRO* 3.4 14.8 - - + +
70B LEU 3.1 0.2 - - - -
71B LYS* 1.3 78.4 - - - +
73B TYR* 1.3 61.7 + - - +
75B ILE* 3.9 8.3 - - - +
76B SER* 3.2 23.6 + - - -
149B LYS* 4.5 26.3 - - + +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO 3.6 1.4 + - - -
70B LEU 2.9 9.0 + - - +
72B ALA* 1.3 78.4 - - - +
74B LEU* 1.3 72.2 + - + +
76B SER* 2.6 36.1 + - - -
78B GLU* 3.8 33.3 + - - +
79B PHE* 3.3 42.0 - + + +
82B LEU* 4.5 5.7 - - - +
142B ALA* 4.3 1.8 - - + -
147B ARG* 3.6 59.8 + - + +
148B VAL* 3.9 25.8 - - - -
149B LYS* 4.1 7.8 - - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.5 28.3 - - + +
55B LEU* 3.7 34.3 - - + -
70B LEU* 3.0 16.7 + - + +
71B LYS* 3.2 7.2 + - - +
73B TYR* 1.3 83.3 - - + +
75B ILE* 1.3 58.8 + - - +
79B PHE* 3.2 33.0 - - + -
80B PHE* 3.9 7.8 - - - -
139B ILE* 4.3 14.6 - - + -
142B ALA* 3.8 28.0 - - + -
143B ILE* 3.9 18.6 - - + +
147B ARG 6.0 0.2 - - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASN* 3.5 38.6 - - + +
51B ILE* 4.5 13.5 - - + -
71B LYS* 2.9 48.6 + - + +
72B ALA* 3.9 7.4 - - - +
74B LEU* 1.3 78.0 - - - +
76B SER* 1.3 61.3 + - - +
77B GLU 3.9 0.7 + - - -
80B PHE* 3.0 31.6 - - + -
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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