Contacts of the helix formed by residues 93 - 101 (chain B) in PDB entry 1YF9
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 CYS 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ASN* 2.9 23.8 + - + +
92B VAL* 1.3 72.3 - - - +
94B LEU* 1.3 68.5 + - - +
95B ASP* 3.7 15.3 - - - -
96B VAL* 3.1 45.4 - - + +
97B ILE* 3.2 7.4 + - - +
125B SER* 3.9 14.4 - - - -
126B ASP 4.7 5.8 - - - -
128B LEU* 3.6 28.7 - - + +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 6.0 4.3 - - - +
71B SER* 5.9 2.5 - - - +
72B PRO 5.7 0.9 - - - +
73B SER* 4.9 18.4 - - - -
91B SER* 5.9 2.5 - - - +
92B VAL 3.2 10.2 + - - +
93B CYS* 1.3 73.2 - - - +
95B ASP* 1.3 58.2 + - - +
97B ILE* 3.3 12.9 + - + +
98B ASN* 2.9 43.6 + - - +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B CYS* 3.3 12.0 - - - -
94B LEU* 1.3 79.6 - - - +
96B VAL* 1.3 60.6 + - - +
98B ASN* 3.4 8.2 + - - +
99B GLN* 3.1 39.1 + - - +
125B SER* 2.8 25.4 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 4.0 9.2 - - + +
92B VAL* 3.9 11.0 - - + -
93B CYS* 3.1 37.0 + - + +
95B ASP* 1.3 74.8 - - - +
97B ILE* 1.3 65.1 + - - +
99B GLN* 3.3 21.2 + - - +
100B THR* 3.7 2.8 + - - -
114B PHE* 3.7 29.1 - - + -
118B LEU* 4.4 8.5 - - + -
123B ASN* 3.8 26.3 + - + +
125B SER* 3.7 28.5 - - - -
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Residues in contact with ILE 97 (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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71B SER* 3.6 30.1 - - - +
72B PRO* 3.9 14.8 - - + +
73B SER* 4.7 1.6 - - - -
74B ILE* 3.9 30.3 - - + +
92B VAL* 3.8 28.5 - - + +
93B CYS 3.2 8.4 + - - +
94B LEU* 3.7 13.0 - - + +
96B VAL* 1.3 76.4 - - - +
98B ASN* 1.3 57.6 + - - +
100B THR* 3.0 7.4 + - - -
101B TRP* 2.8 27.7 + - + -
110B ILE* 5.2 10.4 - - + +
114B PHE* 3.8 26.2 - - + -
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Residues in contact with ASN 98 (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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71B SER* 3.2 28.1 + - - -
94B LEU* 2.9 31.6 + - - +
95B ASP* 3.9 8.5 - - - +
96B VAL 3.3 0.2 - - - -
97B ILE* 1.3 74.6 - - - +
99B GLN* 1.3 61.7 + - - +
100B THR 3.4 0.2 + - - -
101B TRP* 3.6 17.3 - - - +
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Residues in contact with GLN 99 (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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95B ASP* 3.1 39.8 + - - +
96B VAL* 3.6 9.0 - - - +
97B ILE 3.2 0.4 - - - -
98B ASN* 1.3 77.1 - - - +
100B THR* 1.3 60.5 + - - +
101B TRP 5.0 0.4 - - - +
102B THR* 6.1 0.3 - - - +
123B ASN* 3.0 28.3 + - - +
125B SER* 4.6 1.2 - - - +
16C ARG* 2.9 35.4 + - - +
104C MET* 5.2 9.9 - - - +
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Residues in contact with THR 100 (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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96B VAL 3.7 1.8 + - - -
97B ILE 3.0 7.6 + - - -
99B GLN* 1.3 83.4 - - - +
101B TRP* 1.3 65.8 + - - +
102B THR* 3.5 8.9 + - - +
105B TYR* 3.3 46.2 - - + +
110B ILE* 5.5 2.5 - - + -
114B PHE* 3.6 31.7 - - + -
106C GLN* 5.5 8.2 + - - +
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Residues in contact with TRP 101 (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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67B TYR* 3.5 39.9 - + - -
68B PRO* 2.8 32.6 + - + -
69B PHE 4.8 4.3 - - - -
70B LYS 4.4 0.4 - - - -
71B SER* 3.4 31.8 - - - +
72B PRO* 3.6 27.8 - - + -
97B ILE* 2.8 23.0 + - + +
98B ASN* 3.6 15.0 + - - +
99B GLN 3.8 0.6 - - - -
100B THR* 1.3 75.8 - - - +
102B THR* 1.3 91.3 + - - +
103B PRO* 4.4 0.7 - - + -
105B TYR* 3.6 44.6 - + - -
107B LEU* 4.4 6.7 - - + -
110B ILE* 4.0 18.6 - - + +
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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