Contacts of the strand formed by residues 73 - 79 (chain K) in PDB entry 5XVO
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 PRO 73 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41K LEU* 6.1 0.4 - - + -
65K LEU* 5.6 4.5 - - + -
66K PHE 3.4 10.8 - - - +
67K CYS* 3.8 8.7 - - - -
71K ARG 4.2 2.7 - - - +
72K LEU* 1.3 92.1 - - + +
74K ILE* 1.3 62.8 + - - +
188K ALA* 3.8 27.1 - - + +
189K ARG* 4.0 11.9 - - + +
192K VAL* 3.6 28.7 - - + -
211K PHE* 4.4 2.4 - - + -
80L PHE* 4.1 16.6 - - + -
81L TYR* 3.4 23.0 - - - +
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Residues in contact with ILE 74 (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* 2.9 15.5 + - + +
67K CYS 3.8 18.4 - - - +
68K ASP* 3.8 25.6 - - + +
72K LEU* 3.9 1.6 - - + +
73K PRO* 1.3 79.5 - - - +
75K GLY* 1.3 62.6 + - - +
211K PHE* 6.5 0.2 - - + -
55L LYS* 3.9 35.4 - - + +
58L ILE* 4.0 30.0 - - + +
59L ASP* 5.6 3.4 - - - +
79L PRO* 3.5 6.2 - - - +
80L PHE* 3.0 24.7 + - - +
81L TYR* 4.5 10.2 + - + +
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Residues in contact with GLY 75 (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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65K LEU* 3.7 2.1 - - - +
66K PHE* 3.0 31.9 + - - +
74K ILE* 1.3 87.5 - - - +
76K LYS* 1.3 62.9 + - - +
58L ILE* 4.7 3.8 - - - -
77L ILE* 5.2 0.2 - - - -
78L LEU 3.2 13.7 - - - -
79L PRO* 4.2 1.1 - - - -
80L PHE* 3.3 18.5 - - - -
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Residues in contact with LYS 76 (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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63K LEU* 4.1 18.8 - - + -
64K VAL 3.2 15.7 - - - +
65K LEU* 3.7 11.4 - - + -
66K PHE* 4.1 9.1 - - - -
75K GLY* 1.3 75.5 - - - +
77K ILE* 1.3 75.3 + - - +
78K LEU* 5.1 5.1 - - - +
79K PRO* 5.9 1.1 - - - -
86K SER* 5.6 3.7 + - - -
87K SER* 5.0 5.3 + - - +
77L ILE* 3.7 2.1 - - - +
78L LEU* 2.8 55.8 + - + +
80L PHE* 3.9 20.1 - - + -
199L GLN* 4.3 10.7 - - - +
210L ASP* 4.1 18.7 + - - -
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Residues in contact with ILE 77 (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 LEU* 3.6 31.4 - - + +
58K ILE* 3.8 36.1 - - + -
62K ILE 5.9 0.7 - - - +
63K LEU* 5.4 2.9 - - - +
64K VAL* 3.3 34.9 + - + +
66K PHE* 3.9 19.0 - - + -
76K LYS* 1.3 88.0 - - - +
78K LEU* 1.3 70.3 + - - +
79K PRO* 3.5 12.4 - - + +
66L PHE* 3.9 21.1 - - + -
76L LYS 3.6 7.4 - - - +
77L ILE* 4.7 0.7 - - + +
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Residues in contact with LEU 78 (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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76K LYS* 3.7 4.4 + - - -
77K ILE* 1.3 73.8 - - - +
79K PRO* 1.3 78.8 - - + +
80K PHE* 4.7 5.6 - - + -
75L GLY* 3.3 1.4 - - - -
76L LYS* 2.7 57.2 + - + +
78L LEU* 4.0 36.1 - - + -
188L ALA* 5.3 4.9 - - + -
198L THR* 5.2 2.9 - - - +
210L ASP* 3.6 37.5 - - + +
211L PHE* 4.3 22.4 - - + -
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Residues in contact with PRO 79 (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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58K ILE* 3.9 26.0 - - + -
61K LYS* 3.9 25.6 - - + +
62K ILE 6.0 2.5 - - - +
76K LYS* 5.9 1.6 - - - -
77K ILE* 3.5 14.6 - - + +
78K LEU* 1.3 96.0 - - + +
80K PHE* 1.3 62.9 + - - +
81K TYR 3.4 0.2 - - - -
82K GLY 3.8 23.4 - - - +
83K ARG* 5.1 6.3 - - + -
84K HIS 5.9 0.2 - - - +
74L ILE 3.6 6.5 - - - +
75L GLY* 4.2 1.6 - - - -
210L ASP* 5.8 0.2 - - - +
211L PHE* 3.6 12.1 - - - -
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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