Contacts of the strand formed by residues 86 - 92 (chain K) in PDB entry 5M5X
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 VAL 86 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A ARG* 2.8 25.2 + - - +
80K ILE* 3.2 41.3 - - + +
81K MET* 4.6 11.0 - - - +
83K ASN* 3.1 24.9 + - + +
84K PRO 3.3 1.4 - - - +
85K ASP* 1.3 79.5 - - - +
87K GLU* 1.3 59.3 + - - +
88K PHE 3.8 15.0 - - - +
89K CYS* 4.1 16.4 - - + +
105K ILE* 4.4 6.3 - - + -
106K GLN 3.2 16.8 - - - +
107K THR* 5.3 0.2 - - - +
108K TYR* 3.4 8.7 - - - -
116K ALA* 5.0 2.7 - - + -
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Residues in contact with GLU 87 (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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689A ARG* 3.4 7.2 + - - +
693A GLN* 3.0 20.4 + - - -
711A LYS* 6.1 4.5 - - - +
714A THR* 4.6 14.1 + - - +
77H ARG* 4.8 13.0 + - - -
79H TRP 5.6 1.0 - - - +
86K VAL* 1.3 73.2 - - - +
88K PHE* 1.3 59.0 + - - +
106K GLN* 2.8 20.7 + - + +
107K THR* 3.5 32.8 - - - +
108K TYR* 2.9 45.1 + - + +
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Residues in contact with PHE 88 (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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693A GLN* 3.3 58.6 - - + -
696A ILE* 3.6 24.9 - - + -
697A TYR* 3.6 27.6 - + + -
712A ILE* 4.5 15.7 - - + +
714A THR* 4.3 15.7 - - + -
86K VAL* 3.7 1.9 - - - -
87K GLU* 1.3 80.3 - - - +
89K CYS* 1.3 64.6 + - - +
104K ARG* 3.7 22.4 - - + -
105K ILE* 3.5 0.3 - - - -
106K GLN* 2.5 63.1 + - - +
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Residues in contact with CYS 89 (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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690A GLU 5.6 0.3 - - - +
693A GLN* 3.3 28.0 + - - +
694A GLN* 4.3 1.2 + - - +
77K ARG* 4.4 15.9 - - - +
80K ILE* 3.5 28.9 - - + -
81K MET* 3.6 20.9 - - + +
86K VAL* 4.1 10.1 - - + -
88K PHE* 1.3 84.5 - - - +
90K GLY* 1.3 72.8 + - - +
103K ILE* 4.8 8.7 - - - -
104K ARG 3.2 18.4 - - - +
105K ILE* 4.7 3.8 - - + -
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Residues in contact with GLY 90 (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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694A GLN* 4.7 10.8 - - - -
697A TYR* 3.1 20.5 - - - -
77K ARG* 4.6 8.1 - - - -
89K CYS* 1.3 85.7 - - - +
91K TYR* 1.3 58.2 + - - -
103K ILE* 3.6 2.0 - - - -
104K ARG* 2.7 37.3 + - - +
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Residues in contact with TYR 91 (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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694A GLN* 3.1 56.2 + - + +
697A TYR* 3.8 2.6 - - - -
698A GLY* 4.3 5.0 + - - -
1018B THR* 4.2 16.6 - - - +
70K HIS* 3.2 34.9 + + + -
73K GLY* 4.1 25.1 - - - +
74K ASN* 2.7 30.7 + - - -
77K ARG* 4.0 18.1 + - + -
90K GLY* 1.3 74.9 - - - -
92K SER* 1.3 67.2 + - - +
93K ILE* 5.2 2.2 - - + -
101K LEU* 4.1 21.3 - - + -
102K ASN 3.4 8.7 - - - +
103K ILE* 4.5 7.0 - - + +
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Residues in contact with SER 92 (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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697A TYR* 3.6 30.3 - - - -
698A GLY* 3.8 8.2 - - - -
701A ARG* 2.4 42.8 + - - +
91K TYR* 1.3 78.1 - - - +
93K ILE* 1.3 62.6 + - - +
94K PRO* 3.7 1.4 - - - +
101K LEU* 4.2 1.3 - - - +
102K ASN* 2.9 35.7 + - - +
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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