Contacts of the strand formed by residues 91 - 94 (chain G) in PDB entry 3O65
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 GLU 91 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G SER* 5.9 0.9 - - - -
85G LEU* 5.1 2.2 - - - -
86G LYS* 5.8 1.8 - - + -
90G LEU* 1.3 76.9 - - - +
92G ILE* 1.3 67.2 + - + +
93G ILE* 3.2 29.9 - - + +
165G VAL 3.6 0.3 - - - +
166G VAL* 3.5 9.1 - - - +
167G LYS* 3.0 39.8 + - + +
11H LYS* 4.0 14.4 + - - +
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Residues in contact with ILE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 3.5 33.7 - - + -
81G ILE* 4.1 20.4 - - + -
82G SER* 3.7 30.2 + - - +
85G LEU* 4.5 13.0 - - + -
91G GLU* 1.3 79.4 - - + +
93G ILE* 1.3 67.4 + - - +
94G HIS* 5.7 1.0 + - - -
114G ILE* 5.2 7.2 - - + -
164G PHE* 3.5 32.4 - - + -
165G VAL 3.6 4.0 - - - +
166G VAL* 5.0 3.1 - - + +
11H LYS* 3.8 9.0 + - - -
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Residues in contact with ILE 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 3.2 26.9 - - + +
92G ILE* 1.3 76.9 - - - +
94G HIS* 1.3 74.9 + - - +
97G ASN* 3.7 27.1 - - + +
100G TYR* 4.3 8.1 - - + -
164G PHE* 3.5 4.7 - - - -
165G VAL* 2.8 53.1 + - + +
167G LYS* 5.4 9.2 - - + -
11H LYS* 3.2 29.8 - - + +
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Residues in contact with HIS 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 5.8 0.2 - - + -
92G ILE 4.3 1.2 + - - -
93G ILE* 1.3 82.3 - - - +
95G PHE* 1.3 63.8 + - - +
96G ASN* 4.1 6.1 - - - +
97G ASN* 3.2 18.2 - - + +
100G TYR* 4.5 3.8 - - - -
162G SER* 3.8 17.0 - - - -
163G VAL 4.1 3.6 - - - -
164G PHE* 3.1 37.1 - + - -
165G VAL* 4.7 0.3 - - - +
11H LYS* 5.6 1.6 + - - +
34H GLU 4.3 11.1 + - - +
35H GLY 3.7 25.6 - - - +
36H ILE* 3.7 27.5 - - + +
37H PRO* 4.2 2.7 - - + +
40H GLN* 3.6 18.6 + - - -
71H LEU* 4.6 13.0 - - + -
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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