Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 1YAA
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 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY 3.4 10.1 - - - +
76B LEU* 1.3 88.9 - - + +
78B SER* 1.3 54.9 + - - +
80B THR* 3.2 9.5 + - + +
81B SER* 2.6 42.3 + - - -
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Residues in contact with SER 78 (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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76B LEU* 3.2 13.2 - - - -
77B PRO* 1.3 79.3 - - - +
79B LEU* 1.3 61.9 + - - +
81B SER* 3.8 4.3 - - - -
82B ASN* 2.8 33.7 + - - +
307B ALA* 3.5 15.4 - - - +
311B GLU* 2.8 37.0 + - - +
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Residues in contact with LEU 79 (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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76B LEU* 3.1 15.3 + - + +
78B SER* 1.3 78.2 - - - +
80B THR* 1.3 60.0 + - - +
82B ASN* 3.8 0.7 - - - +
83B ALA* 2.8 33.9 + - + +
104B GLN* 3.5 39.0 - - + +
256B PHE* 4.7 6.1 - - + -
267B VAL* 4.0 15.7 - - + -
268B GLY 4.5 0.2 - - - +
269B CYS* 3.9 16.2 - - - -
303B ALA* 3.6 25.4 - - + +
306B VAL* 3.8 35.4 - - + -
307B ALA* 4.0 7.6 - - - +
310B LEU* 4.5 2.5 - - + +
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Residues in contact with THR 80 (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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74B THR 4.0 9.0 - - - +
76B LEU 3.1 11.8 + - - +
77B PRO* 3.2 16.8 + - - +
79B LEU* 1.3 75.8 - - + +
81B SER* 1.3 69.7 + - - +
83B ALA* 3.7 0.9 - - - +
84B ALA* 3.1 26.2 + - - +
102B SER* 4.0 24.2 + - - +
103B VAL 4.0 5.2 - - - -
104B GLN* 3.6 34.5 - - + +
269B CYS* 4.0 14.7 - - - -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 2.6 29.3 + - - -
78B SER* 3.4 8.0 + - - -
80B THR* 1.3 75.4 + - - +
82B ASN* 1.3 70.9 + - - +
84B ALA* 3.5 0.6 + - - +
85B LYS* 2.8 47.3 + - - +
102B SER* 5.8 0.4 - - - -
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Residues in contact with ASN 82 (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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78B SER* 2.8 24.6 + - - +
81B SER* 1.3 83.5 + - - +
83B ALA* 1.3 65.0 + - - +
85B LYS* 3.2 23.1 + - - +
86B ILE* 3.4 13.7 + - - +
307B ALA 4.1 4.6 + - - -
310B LEU* 3.7 29.3 - - + +
311B GLU* 3.3 32.4 - - - +
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Residues in contact with ALA 83 (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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79B LEU* 2.8 24.4 + - + +
80B THR 3.7 2.0 - - - +
82B ASN* 1.3 72.7 - - - +
84B ALA* 1.3 63.2 + - - +
86B ILE* 3.1 23.5 + - - +
87B ILE* 3.4 2.9 + - - +
254B GLN* 3.4 31.9 + - - +
256B PHE* 4.1 9.0 - - + -
269B CYS* 3.6 19.7 - - - -
310B LEU* 3.8 9.8 - - + +
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Residues in contact with ALA 84 (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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80B THR 3.1 13.9 + - - +
81B SER* 3.8 5.2 - - - +
82B ASN 3.3 0.2 - - - -
83B ALA* 1.3 76.2 - - - +
85B LYS* 1.3 61.9 + - - +
87B ILE 4.7 0.2 - - - +
88B PHE* 3.0 47.7 + - + +
95B LEU* 3.8 14.3 - - + +
102B SER* 3.7 10.3 - - - +
269B HIS* 3.5 26.4 - - - +
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Residues in contact with LYS 85 (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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81B SER* 2.8 39.6 + - - +
82B ASN* 3.2 16.4 + - - +
83B ALA 3.1 0.6 - - - -
84B ALA* 1.3 79.4 - - - +
86B ILE* 1.3 58.6 + - + +
89B GLY* 3.0 31.4 + - - +
90B THR* 3.9 18.7 + - + +
95B LEU* 3.6 37.6 - - + +
241B ARG* 4.5 0.3 + - - -
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Residues in contact with ILE 86 (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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82B ASN 3.4 10.9 + - - +
83B ALA 3.1 19.7 - - - +
85B LYS* 1.3 78.6 - - + +
87B ILE* 1.3 58.3 + - - +
226B GLN* 3.0 34.9 + - - +
233B LEU* 5.0 11.5 - - + +
241B ARG* 3.1 14.2 + - - +
254B GLN* 3.4 19.3 - - - +
256B PHE* 3.8 22.7 - - + -
259B ASN* 5.4 1.3 - - - +
310B LEU* 4.0 18.8 - - + -
316B THR* 6.4 1.3 - - + -
319B TRP* 4.0 19.5 - - + -
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Residues in contact with ILE 87 (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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83B ALA 3.4 3.5 + - - +
84B ALA 4.0 5.4 - - - +
85B LYS 3.3 0.4 - - - -
86B ILE* 1.3 78.2 - - - +
88B PHE* 1.3 73.6 + - + +
223B THR* 3.9 24.5 - - + -
226B GLN* 3.2 26.2 - - - +
237B ALA* 3.6 8.0 - - + +
240B VAL* 3.9 20.5 - - + +
241B ARG* 2.9 26.0 + - - +
252B VAL* 3.8 22.0 - - + -
254B GLN* 3.2 40.8 - - + +
269B HIS* 4.5 2.2 - - - +
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Residues in contact with PHE 88 (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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84B ALA* 3.0 29.1 + - + +
87B ILE* 1.3 83.9 - - + +
89B GLY* 1.3 59.6 + - - +
92B SER* 3.5 25.6 - - - +
95B LEU* 3.9 12.6 - - + -
100B VAL* 3.5 32.5 - - + -
240B VAL* 4.9 1.6 - - + -
241B ARG* 3.6 19.9 + - - +
242B VAL* 3.9 34.5 - - - +
252B VAL* 4.1 19.1 - - + -
269B ALA* 3.4 57.2 - - - -
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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