Contacts of the helix formed by residues 91 - 100 (chain B) in PDB entry 5Y1Z
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 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLN 5.6 1.8 - - - +
89B ASP 3.7 5.6 - - - +
90B VAL* 1.3 94.2 - - + +
92B ASP* 1.3 66.1 + - - +
93B ALA* 3.3 3.1 - - + +
94B ARG* 3.1 17.3 + - + +
95B LYS* 3.0 19.4 + - - +
233D LYS* 5.3 4.3 - - - +
236D GLN* 5.8 5.2 - - - +
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Residues in contact with ASP 92 (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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90B VAL 4.3 0.7 - - - +
91B PRO* 1.3 71.8 - - - +
93B ALA* 1.3 64.1 + - - +
95B LYS* 3.1 30.7 + - - +
96B CYS* 2.9 23.4 + - - +
169D GLY* 6.1 0.3 - - - -
233D LYS* 3.5 32.2 + - + +
237D ILE* 4.0 9.1 - - + +
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Residues in contact with ALA 93 (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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91B PRO* 3.3 3.0 - - + +
92B ASP* 1.3 79.0 - - - +
94B ARG* 1.3 57.3 + - - +
96B CYS* 3.4 2.8 + - - +
97B ALA* 2.9 26.9 + - - +
233D LYS 5.2 0.7 - - - +
236D GLN* 3.7 50.3 - - + +
237D ILE* 3.5 14.3 - - + +
240D VAL* 3.6 7.8 - - + +
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Residues in contact with ARG 94 (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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-1B GLY* 3.9 23.9 - - - +
34B TYR* 3.7 23.4 - - - +
38B SER 3.5 15.1 + - - -
39B ASP* 2.7 30.5 + - - -
63B VAL* 5.0 1.5 - - + +
90B VAL* 3.9 16.6 - - + -
91B PRO* 3.1 22.3 + - + +
93B ALA* 1.3 77.6 - - - +
95B LYS* 1.3 65.2 + - - +
97B ALA* 4.3 7.9 - - - +
98B CYS* 2.9 44.1 + - - +
101B HIS* 4.6 2.0 - - - -
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Residues in contact with LYS 95 (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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63B VAL* 5.1 0.7 - - - -
86B VAL* 3.4 33.6 + - + +
87B GLY 3.2 22.8 + - - -
88B GLU* 3.6 16.4 + - - +
90B VAL* 3.2 27.5 - - + +
91B PRO 3.0 13.3 + - - +
92B ASP* 3.3 27.6 - - - +
94B ARG* 1.3 77.4 - - - +
96B CYS* 1.3 63.9 + - - +
98B CYS* 3.7 4.5 - - - +
99B ALA* 3.0 24.3 + - - +
119B SER* 5.4 2.0 + - - -
168D PRO 5.2 1.1 - - - +
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Residues in contact with CYS 96 (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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92B ASP 2.9 12.8 + - - +
93B ALA 3.5 9.0 - - - +
94B ARG 3.2 0.2 - - - -
95B LYS* 1.3 78.5 - - - +
97B ALA* 1.3 62.3 + - - +
99B ALA* 3.4 12.9 + - - +
100B SER* 3.8 3.1 + - - -
167D GLN* 3.8 13.6 - - - +
168D PRO 3.5 26.2 + - - +
169D GLY* 4.4 2.2 - - - -
170D THR* 3.6 28.7 - - - -
237D ILE* 3.7 20.6 - - + -
240D VAL* 4.1 14.6 - - + +
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Residues in contact with ALA 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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-1B GLY 3.9 24.9 - - - +
93B ALA 2.9 16.9 + - - +
94B ARG* 3.8 16.4 - - - +
95B LYS 3.3 0.2 - - - -
96B CYS* 1.3 77.1 - - - +
98B CYS* 1.3 60.3 + - - +
100B SER* 2.9 26.5 + - - -
101B HIS* 3.5 11.9 + - - +
240D VAL* 3.7 19.6 - - + +
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Residues in contact with CYS 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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34B TYR* 3.6 29.4 - - - +
63B VAL* 3.9 26.7 - - + -
65B TYR* 3.5 6.6 + - - -
86B VAL* 6.2 1.3 - - + -
94B ARG* 2.9 53.6 + - - +
95B LYS 3.8 2.9 - - - +
97B ALA* 1.3 77.7 - - - +
99B ALA* 1.3 57.6 + - - +
101B HIS* 2.8 32.7 + - - +
102B VAL* 3.5 3.7 + - - +
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Residues in contact with ALA 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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84B ASN* 5.9 1.8 - - - +
95B LYS 3.0 13.0 + - - +
96B CYS* 3.6 12.1 - - - +
97B ALA 3.2 0.4 - - - -
98B CYS* 1.3 77.4 - - - +
100B SER* 1.3 61.1 + - - +
101B HIS 3.2 0.9 + - - -
102B VAL* 3.3 24.8 + - - +
103B ALA 4.8 0.5 + - - -
167D GLN* 3.3 19.4 - - + +
168D PRO* 4.1 20.4 - - + +
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Residues in contact with SER 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 CYS 3.8 1.0 + - - -
97B ALA* 2.9 18.8 + - - -
99B ALA* 1.3 77.1 - - - +
101B HIS* 1.3 67.9 + - - +
102B VAL 3.5 0.2 - - - -
103B ALA* 4.7 5.3 + - - +
104B LYS* 5.0 4.2 + - - +
164D LYS* 4.9 2.2 - - - -
167D GLN* 3.4 23.3 + - - +
244D ILE* 3.9 29.4 - - - +
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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