Contacts of the helix formed by residues 57 - 69 (chain B) in PDB entry 1YCH
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 PHE 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.6 22.7 - - + -
17B VAL 3.7 19.1 - - - -
18B ASP* 3.4 39.3 - - + -
37B TYR* 3.7 14.6 - + - -
53B VAL* 3.4 23.7 - - + +
54B TYR* 2.7 23.9 + + - -
56B PRO* 1.3 85.6 - - + +
58B LYS* 1.3 65.6 + - - +
59B GLU* 3.1 3.8 - - - -
60B GLU* 2.9 26.6 + - + +
61B LEU 3.2 7.8 + - - -
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Residues in contact with LYS 58 (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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54B TYR 3.7 2.0 + - - -
55B GLU* 2.9 43.6 + - + +
56B PRO 3.6 0.2 - - - -
57B PHE* 1.3 77.4 - - - +
59B GLU* 1.3 91.6 + - - +
61B LEU* 3.0 7.2 + - - +
62B ILE* 3.0 30.7 + - + +
89B ALA* 3.8 28.3 - - + -
92B ALA* 4.0 24.5 - - + -
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Residues in contact with GLU 59 (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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56B PRO 3.8 13.2 - - - +
57B PHE* 3.1 0.8 + - - -
58B LYS* 1.3 110.0 + - - +
60B GLU* 1.3 60.4 + - + +
62B ILE* 3.5 7.8 + - - +
63B ALA* 2.8 32.5 + - - +
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Residues in contact with GLU 60 (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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2B SER* 3.6 16.8 + - - +
15B GLY 5.1 0.2 - - - -
16B ALA* 4.2 16.4 - - + -
57B PHE* 2.9 20.9 + - + +
59B GLU* 1.3 78.4 - - + +
61B LEU* 1.3 66.5 + - - +
63B ALA* 3.4 7.7 + - - +
64B LYS* 3.0 55.6 + - - +
610B ZN 2.9 25.9 - - - -
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Residues in contact with LEU 61 (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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14B VAL* 3.5 38.8 - - + +
15B GLY 5.3 0.4 + - - -
16B ALA* 5.5 0.4 - - - +
39B ALA* 4.4 9.2 - - + -
49B LEU* 4.5 4.5 - - + -
52B THR* 4.0 25.4 - - + -
53B VAL* 4.2 16.4 - - + +
57B PHE 3.2 6.9 + - - +
58B LYS* 3.0 11.8 + - - +
60B GLU* 1.3 76.8 - - - +
62B ILE* 1.3 61.1 + - + +
64B LYS* 3.0 4.5 + - - +
65B LEU* 2.8 46.5 + - + +
89B ALA* 4.2 7.9 - - + -
93B ILE* 3.9 26.0 - - + -
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Residues in contact with ILE 62 (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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58B LYS* 3.0 20.4 + - + +
59B GLU* 3.9 6.3 - - - +
61B LEU* 1.3 82.5 - - + +
63B ALA* 1.3 64.2 + - - +
65B LEU* 3.1 9.1 + - + +
66B LYS* 2.9 52.7 + - + +
72B VAL* 5.6 2.0 - - + -
92B ALA* 4.5 28.0 - - + +
93B ILE* 4.2 19.1 - - + -
96B LEU* 5.1 15.3 - - + -
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Residues in contact with ALA 63 (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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2B SER 5.5 2.0 - - - +
59B GLU 2.8 24.8 + - - +
60B GLU* 3.8 11.9 - - - +
62B ILE* 1.3 75.4 - - - +
64B LYS* 1.3 61.8 + - - +
66B LYS* 3.6 7.7 + - - +
67B GLN* 3.3 28.8 + - - +
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Residues in contact with LYS 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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2B SER 3.3 26.8 - - - +
3B GLN 3.6 10.3 - - - -
4B PRO* 3.4 31.8 - - + +
13B TRP* 3.5 21.4 - - + -
14B VAL* 3.7 26.5 - - + +
15B GLY 2.7 29.6 + - - +
16B ALA* 4.4 2.4 - - - +
60B GLU* 3.0 42.7 + - - +
61B LEU 3.5 3.8 - - - +
63B ALA* 1.3 74.3 - - - +
65B LEU* 1.3 66.5 + - - +
67B GLN* 2.9 18.4 + - - +
68B ILE* 3.5 3.8 + - - +
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Residues in contact with LEU 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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14B VAL* 4.0 13.7 - - + -
41B LEU* 3.8 28.6 - - + +
49B LEU* 3.8 28.0 - - + -
61B LEU* 2.8 28.1 + - + +
62B ILE* 3.1 10.1 + - - +
64B LYS* 1.3 75.4 - - - +
66B LYS* 1.3 58.2 + - - +
68B ILE* 2.9 24.7 + - - +
69B LYS 3.3 10.4 + - - +
72B VAL* 3.9 29.3 - - + +
74B LEU* 4.5 3.8 - - + -
93B ILE* 3.8 28.7 - - + -
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Residues in contact with LYS 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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62B ILE* 2.9 37.8 + - + +
63B ALA* 3.9 8.1 - - - +
65B LEU* 1.3 75.5 - - - +
67B GLN* 1.3 61.6 + - - +
68B ILE 3.4 0.3 + - - -
69B LYS 3.6 10.5 + - - -
70B ASP* 3.5 49.5 + - - +
71B PRO* 5.9 0.4 - - - -
72B VAL* 3.6 22.0 - - + +
96B LEU* 4.7 15.3 - - - +
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Residues in contact with GLN 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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2B SER* 2.7 32.2 + - - +
3B GLN* 4.0 17.6 - - - +
4B PRO* 3.8 15.1 - - + +
63B ALA* 3.3 16.7 + - - +
64B LYS 2.9 12.3 + - - +
65B LEU 2.9 0.4 + - - -
66B LYS* 1.3 78.4 - - - +
68B ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 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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4B PRO* 4.0 18.2 - - + -
12B TYR* 3.4 59.5 - - + +
14B VAL* 4.8 2.2 - - + -
41B LEU* 3.9 24.5 - - + -
43B VAL* 3.9 12.1 - - + -
64B LYS 3.9 11.4 - - - +
65B LEU 2.9 6.8 + - - +
66B LYS 4.3 0.2 - - - -
67B GLN* 1.3 83.6 - - - +
69B LYS* 1.3 65.8 + - + +
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Residues in contact with LYS 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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41B LEU* 6.4 0.2 - - + -
65B LEU 3.3 10.9 + - - +
66B LYS* 3.6 6.3 - - - -
67B GLN 3.6 1.2 - - - -
68B ILE* 1.3 88.9 - - + +
70B ASP* 1.3 78.6 + - - +
71B PRO* 3.7 26.9 + - - +
72B VAL* 3.8 9.4 - - - +
73B LYS* 5.2 15.2 - - + +
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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