Contacts of the strand formed by residues 82 - 86 (chain K) in PDB entry 6R1U
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 TRP 82 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50K SER* 3.4 23.0 + - - -
51K ARG* 4.1 8.6 - - - +
52K LYS 3.6 27.3 + - - +
53K CYS* 4.3 7.8 - - + -
54K GLU* 3.1 29.5 + - - +
63K PRO* 3.6 30.4 - - + +
64K VAL 3.6 5.8 - - - -
65K CYS* 3.4 24.0 - - + -
74K ALA* 4.6 2.7 - - + -
75K LYS 2.9 30.3 - - - -
77K GLY 3.6 17.5 + - - -
79K THR* 3.5 18.4 - - + +
81K ARG* 1.3 72.5 - - - +
83K TYR* 1.3 60.7 - - - +
90K HIS* 3.9 14.8 - - + -
91K PHE* 3.6 6.7 - - - -
92K CYS* 3.4 37.0 - - + -
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Residues in contact with TYR 83 (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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54K GLU* 3.4 15.0 - - - +
81K ARG* 3.7 42.7 + - + -
82K TRP* 1.3 72.6 - - - +
84K HIS* 1.3 59.7 + - - +
90K HIS* 3.1 9.3 - - - -
91K PHE* 2.9 67.9 + + + +
93K ASN* 3.0 36.8 + - - -
96K PHE* 3.6 49.5 - + + -
128K LYS* 4.3 10.8 - - + -
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Residues in contact with HIS 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K CYS* 3.6 11.0 - - - -
54K GLU* 2.8 15.7 + - - +
55K LYS* 3.7 24.5 - - + +
58K CYS* 4.2 3.8 - - + -
83K TYR* 1.3 72.6 - - - +
85K LEU* 1.3 63.1 + - - +
86K SER* 3.0 30.3 + - - -
87K CYS* 3.5 6.1 - - - -
90K HIS* 3.6 5.2 - - - -
128K LYS* 2.9 26.4 + - - +
204K MET* 2.7 29.2 + - + -
206K ILE* 3.2 26.4 - - + +
902K ZN 2.4 36.3 - - - -
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Residues in contact with LEU 85 (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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66K PHE* 3.7 31.2 - - + -
83K TYR 4.0 0.6 + - - -
84K HIS* 1.3 82.4 - - - +
86K SER* 1.3 61.6 + - - +
89K GLU* 3.0 22.1 + - + +
91K PHE* 3.6 22.2 - - + -
128K LYS* 3.8 26.7 - - + +
131K MET* 3.9 13.5 - - + -
132K ALA* 4.0 10.8 - - + +
136K LEU* 3.9 20.4 - - + -
205K LEU* 3.2 25.8 - - + +
206K ILE* 3.3 16.8 + - + +
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Residues in contact with SER 86 (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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84K HIS* 3.0 23.9 + - - -
85K LEU* 1.3 79.6 - - - +
87K CYS* 1.3 65.6 + - - +
88K GLY* 3.0 11.9 + - - -
89K GLU* 2.7 42.8 + - - +
90K HIS* 3.6 2.3 - - - -
201K TRP* 3.7 27.8 - - - -
204K MET 3.9 4.7 - - - -
205K LEU* 4.5 7.4 - - - -
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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