Contacts of the strand formed by residues 92 - 95 (chain K) in PDB entry 6CU0
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 PHE 92 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 4.1 22.2 - - + -
156B GLU* 4.9 3.8 - - - -
71K VAL* 4.4 17.5 - - + -
88K CYS* 4.0 7.0 - - + +
89K THR* 3.2 38.1 + - - +
90K PRO* 4.3 6.4 - - - +
91K GLY* 1.3 81.5 + - - +
93K HIS* 1.3 62.0 + - - +
102K CYS* 4.0 19.5 - - + -
103K GLU* 3.2 13.0 - - - +
104K GLN* 3.5 33.4 - - + -
105K ASP* 3.4 8.9 - - - +
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Residues in contact with HIS 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K CYS* 3.5 8.7 - - - -
92K PHE* 1.3 74.8 - - - +
94K CYS* 1.3 77.2 + - - +
95K LEU* 4.5 5.4 - - + +
102K CYS* 3.6 1.0 - - - -
103K GLU* 2.8 71.1 + - + +
104K GLN 3.7 10.1 + - - -
105K ASP* 3.4 25.6 - - - +
106K CYS* 4.1 4.9 - - - -
112K LEU* 5.0 11.0 - - + +
113K THR 5.9 0.9 - - - -
116K GLY* 5.3 0.7 - - - -
117K CYS* 3.7 15.7 - - - -
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Residues in contact with CYS 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K CYS 4.2 1.1 - - - -
87K ASP* 4.0 8.5 - - - -
88K CYS* 3.4 18.4 - - - +
93K HIS* 1.3 90.1 + - - +
95K LEU* 1.3 61.8 + - - +
96K GLY 5.4 0.9 - - - +
99K CYS* 2.0 53.4 - - + -
101K MET 4.0 0.4 - - - -
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Residues in contact with LEU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ALA* 4.5 12.6 - - + -
93K HIS* 4.5 6.7 - - + +
94K CYS* 1.3 83.1 - - - +
96K GLY* 1.3 66.2 + - - +
99K CYS* 4.4 0.6 - - - -
100K SER* 3.0 25.2 + - - -
101K MET* 3.0 34.1 + - + +
103K GLU* 3.5 32.1 - - + +
113K THR 4.3 6.1 - - - +
114K LYS 3.7 21.8 - - - +
115K LYS 4.8 4.5 - - - +
116K GLY* 3.8 20.9 - - - +
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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