Contacts of the strand formed by residues 69 - 74 (chain t) in PDB entry 4PJO
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 69 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80s LYS* 3.0 38.5 - - + +
82s ASP* 4.4 0.5 - - - +
83s ASN* 4.2 0.2 + - - -
21t VAL* 4.5 9.0 - - + -
22t LYS 3.9 9.0 - - - +
23t LEU* 4.1 8.1 - - + -
24t LYS* 3.7 15.2 - - - -
40t MET 4.6 0.2 - - - +
42t MET* 3.9 30.7 - - + -
64t ILE* 5.0 6.3 - - + -
65t ARG 4.1 0.6 + - - -
66t CYS* 2.9 28.1 + - - +
68t ASN* 1.3 80.0 - - - +
70t LEU* 1.3 64.5 + - - +
71t TYR 4.0 18.4 - - - +
72t ILE* 5.5 0.2 - - + -
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Residues in contact with LEU 70 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35s LEU* 4.4 9.2 - - + -
38s GLN* 5.4 0.9 - - - +
41s MET* 4.1 21.8 - - + -
43s ILE* 4.8 2.7 - - + -
79s LEU* 3.7 16.1 - - + -
80s LYS* 3.0 25.6 + - - +
83s ASN* 3.3 39.3 + - + +
22t LYS* 2.7 34.2 + - + +
23t LEU 4.7 3.1 - - - +
24t LYS* 3.8 18.6 - - + +
68t ASN 3.7 1.2 + - - -
69t VAL* 1.3 73.9 - - - +
71t TYR* 1.3 80.3 + - + +
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Residues in contact with TYR 71 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43s ILE* 3.8 23.3 - - + -
63s GLU* 2.7 29.5 + - - -
74s LEU* 3.4 19.2 - - + +
77s ILE* 4.2 14.8 - - + -
78s MET 3.1 17.0 - - - +
79s LEU* 4.0 7.9 - - + -
80s LYS* 5.4 0.7 - - - -
20t MET* 5.1 2.7 - - + -
21t VAL* 3.5 1.4 - - - -
22t LYS* 2.8 62.2 + - + +
28t GLU* 4.7 5.9 + - - -
69t VAL* 4.0 6.4 - - - +
70t LEU* 1.3 94.2 - - + +
72t ILE* 1.3 72.1 + - - +
73t ARG* 4.1 26.5 + - + -
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Residues in contact with ILE 72 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77s ILE* 3.4 3.3 - - - +
78s MET* 2.9 58.0 + - + +
80s LYS* 6.2 0.7 - - + -
10t PHE* 4.2 4.6 - - + -
11t LEU* 3.8 22.9 - - + -
14t LEU* 4.5 4.3 - - + -
19t VAL* 3.1 30.1 - - + -
20t MET 3.6 4.7 - - - -
21t VAL* 3.5 20.9 - - + +
33t LEU* 3.7 24.5 - - + -
42t MET* 3.9 17.0 - - + -
44t LEU* 6.1 0.2 - - + -
69t VAL* 5.5 0.4 - - + -
71t TYR* 1.3 77.1 - - - +
73t ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 73 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73s GLN 5.3 2.8 + - - -
74s LEU* 3.6 49.1 + - - +
76s ARG 3.7 15.9 - - - +
77s ILE* 3.7 8.5 - - + -
14t LEU* 4.3 5.6 - - - -
19t VAL* 3.2 7.7 - - - +
20t MET* 2.8 64.4 + - + +
28t GLU* 4.6 5.5 + - - -
71t TYR* 4.1 15.9 + - + -
72t ILE* 1.3 77.6 - - - +
74t GLY* 1.3 74.2 + - - +
75t VAL* 3.7 16.6 + - - -
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Residues in contact with GLY 74 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74s LEU 5.2 1.7 - - - +
76s ARG 3.9 7.9 + - - -
10t PHE* 4.9 0.2 - - - -
14t LEU* 4.1 21.4 - - - +
18t PRO 4.1 5.2 - - - -
19t VAL* 4.4 0.9 - - - -
73t ARG* 1.3 88.8 + - - +
75t VAL* 1.3 70.2 + - - +
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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