Contacts of the strand formed by residues 73 - 79 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41I LEU* 6.1 0.2 - - + -
65I LEU* 5.6 3.8 - - + -
66I PHE 3.4 10.1 - - - +
67I CYS* 3.8 9.6 - - - -
71I ARG 4.2 2.9 - - - +
72I LEU* 1.3 92.3 - - + +
74I ILE* 1.3 62.5 + - - +
188I ALA* 3.9 25.6 - - + +
189I ARG* 4.0 12.3 - - + +
192I VAL* 3.6 35.7 - - + -
211I PHE* 4.5 1.6 - - + -
80J PHE* 4.2 9.4 - - + -
81J TYR* 3.1 30.3 - - - +
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Residues in contact with ILE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I PHE* 2.9 16.1 + - + +
67I CYS 3.8 19.5 - - - +
68I ASP* 3.8 25.6 - - + +
72I LEU* 3.9 1.6 - - + +
73I PRO* 1.3 79.2 - - - +
75I GLY* 1.3 63.0 + - - +
55J LYS* 4.0 25.1 - - + +
58J ILE* 3.9 34.8 - - + +
59J ASP* 5.6 3.6 - - - +
79J PRO* 3.3 8.7 - - - +
80J PHE* 2.9 25.0 + - - +
81J TYR* 4.3 10.7 + - + -
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Residues in contact with GLY 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LEU* 3.7 1.4 - - - -
66I PHE* 2.9 31.7 + - - +
74I ILE* 1.3 88.5 - - - +
76I LYS* 1.3 63.6 + - - +
58J ILE* 4.7 4.3 - - - -
77J ILE* 6.3 0.2 - - - -
78J LEU 3.1 13.0 - - - -
79J PRO* 4.0 1.8 - - - -
80J PHE* 3.3 18.1 - - - -
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Residues in contact with LYS 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 4.1 19.7 - - + -
64I VAL 3.2 15.5 - - - +
65I LEU* 3.8 10.8 - - + -
66I PHE* 4.1 8.4 - - - -
75I GLY* 1.3 75.2 - - - +
77I ILE* 1.3 72.1 + - - +
78I LEU* 5.1 5.7 - - - +
79I PRO* 5.9 0.9 - - - -
86I SER* 5.5 5.1 + - - -
87I SER* 4.9 6.7 + - - +
77J ILE* 3.5 1.9 - - - +
78J LEU* 2.7 60.8 + - + +
80J PHE* 3.8 20.1 - - + -
199J GLN* 4.4 11.1 - - - +
210J ASP* 4.4 16.0 + - - -
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Residues in contact with ILE 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I LEU* 3.6 31.0 - - + +
58I ILE* 3.7 36.6 - - + -
62I ILE 5.9 0.9 - - - +
63I LEU* 5.4 2.8 - - - +
64I VAL* 3.3 33.8 + - + +
66I PHE* 3.9 16.8 - - + -
76I LYS* 1.3 89.4 - - - +
78I LEU* 1.3 69.8 + - - +
79I PRO* 3.5 12.6 - - + +
66J PHE* 3.9 23.1 - - + -
76J LYS 3.5 7.4 - - - +
77J ILE* 4.5 0.4 - - + +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I LYS* 3.7 4.9 + - - +
77I ILE* 1.3 73.6 - - - +
79I PRO* 1.3 79.5 - - + +
80I PHE* 3.6 5.3 + - + -
75J GLY* 3.2 1.2 - - - -
76J LYS* 2.7 56.5 + - + +
78J LEU* 4.0 38.8 - - + -
188J ALA* 5.3 6.1 - - + -
198J THR* 5.2 2.5 - - - +
199J GLN* 6.2 0.2 - - - +
210J ASP* 3.8 36.8 - - + +
211J PHE* 4.4 22.2 - - + -
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Residues in contact with PRO 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 3.9 26.0 - - + +
61I LYS* 4.0 28.3 - - + +
62I ILE 5.9 2.2 - - - +
76I LYS* 5.9 1.3 - - - -
77I ILE* 3.5 14.8 - - + +
78I LEU* 1.3 100.5 - - + +
80I PHE* 1.3 63.5 + - - +
82I GLY 3.9 23.8 - - - +
83I ARG* 5.3 3.1 - - - +
84I HIS 5.8 2.2 - - - +
74J ILE 3.5 6.5 - - - +
75J GLY* 4.2 1.3 - - - -
211J PHE* 3.8 7.3 - - - -
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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