Contacts of the strand formed by residues 86 - 91 (chain G) in PDB entry 4OZH
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 SER 86 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G PRO* 5.9 1.4 - - - +
23G CYS 3.3 14.0 + - - -
24G ASN* 4.3 10.5 + - - -
25G HIS* 3.7 9.9 - - - -
80G ILE* 3.9 3.3 - - - +
81G THR* 3.1 43.6 + - - +
83G ASP* 5.2 0.7 - - - -
84G ARG 3.2 0.8 - - - -
85G LYS* 1.4 80.4 - - - +
87G SER* 1.4 71.8 + - - +
88G THR* 5.1 1.9 + - - -
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Residues in contact with SER 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G PRO* 3.7 1.2 - - - +
23G CYS* 2.9 43.8 + - - +
25G HIS* 2.9 23.6 + - - -
39G VAL* 3.4 20.5 - - - +
41G TRP* 4.3 2.1 + - - -
78G LEU* 4.3 4.5 - - - -
79G ILE 3.3 12.6 - - - -
80G ILE* 4.2 10.3 - - - -
81G THR* 5.4 0.7 - - - -
86G SER* 1.4 80.0 + - - +
88G THR* 1.3 66.2 + - - +
104G CYS* 4.2 0.2 - - - -
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Residues in contact with THR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ASN* 4.0 26.7 - - + +
21G LEU 3.4 14.6 - - - +
22G PRO* 4.6 5.4 - - + +
41G TRP* 5.0 0.7 - - - -
77G SER 3.8 0.3 - - - +
78G LEU* 3.5 8.7 - - - +
79G ILE* 2.9 44.9 + - - +
86G SER* 5.1 2.6 + - - -
87G SER* 1.3 77.4 + - - +
89G LEU* 1.3 64.8 + - - +
90G ILE* 4.1 8.2 + - + -
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Residues in contact with LEU 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ALA 3.2 5.2 - - - +
20G ASN* 3.3 2.3 - - - -
21G LEU* 2.9 58.7 + - + +
41G TRP* 3.6 47.5 - - + -
53G ILE* 4.4 6.5 - - + -
54G ILE* 3.6 31.0 - - + -
76G ALA* 4.2 12.3 - - + -
77G SER 3.4 7.0 - - - +
78G LEU* 4.7 0.7 - - + -
88G THR* 1.3 71.1 - - - +
90G ILE* 1.3 61.4 + - - +
91G LEU* 4.4 9.4 - - + -
102G TYR* 3.9 15.9 - - + -
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Residues in contact with ILE 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ALA* 4.4 11.4 - - + -
19G ALA 3.4 3.1 - - - +
20G ASN* 3.4 24.5 - - - +
76G ALA* 3.3 6.2 - - - +
77G SER* 2.7 47.4 + - - +
79G ILE* 3.7 31.6 - - + -
88G THR* 4.7 7.4 - - + +
89G LEU* 1.3 75.7 - - - +
91G LEU* 1.3 64.7 + - - +
92G PRO* 3.4 19.8 - - + +
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Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ALA* 3.3 0.2 - - - -
19G ALA* 2.9 47.6 + - + +
21G LEU* 4.3 15.5 - - + -
43G ARG* 5.0 2.2 - - - +
53G ILE* 5.4 3.4 - - + -
75G MET* 4.0 21.5 - - + +
76G ALA* 4.0 11.2 - - + -
89G LEU* 4.4 5.2 - - + -
90G ILE* 1.3 73.5 - - - +
92G PRO* 1.4 67.4 - - - +
93G HIS 3.6 2.5 - - - -
94G ALA* 4.0 13.2 + - + -
98G ASP* 4.1 22.9 - - + +
102G TYR* 3.6 39.3 - - + +
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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