Contacts of the strand formed by residues 60 - 65 (chain G) in PDB entry 5D7I
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 PHE 60 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLN* 4.2 14.4 - - - -
46G LEU* 3.9 40.8 - - + -
55G GLU 4.1 0.3 - - - +
56G GLU* 4.2 0.3 - - - +
57G LYS* 2.7 46.6 + - + +
58G GLY 3.1 0.6 - - - -
59G ARG* 1.3 106.6 - - + +
61G SER* 1.3 59.3 + - - +
73G LEU* 4.5 12.3 - - + -
74G LEU 3.3 5.2 - - - +
75G LEU* 3.7 33.2 - - + -
82G ASP* 3.8 18.2 - - - -
86G TYR* 4.2 9.2 - + - -
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Residues in contact with SER 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G LEU* 3.6 25.7 - - - +
55G GLU 3.3 7.9 - - - -
56G GLU* 3.7 18.9 + - - +
60G PHE* 1.3 75.9 + - - +
62G SER* 1.3 61.7 + - - +
63G PHE 4.3 0.2 - - - -
72G TYR 3.7 0.3 - - - +
73G LEU* 3.4 6.1 - - - +
74G LEU* 2.7 56.9 + - - +
76G LYS* 4.3 10.9 + - - -
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Residues in contact with SER 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G TRP* 4.2 9.9 - - - -
47G SER* 3.3 32.1 - - - -
48G TYR 4.8 0.3 + - - -
49G ASN* 2.7 36.7 + - - -
54G LEU* 3.9 2.7 - - - -
55G GLU* 2.9 37.7 + - - +
61G SER* 1.3 74.7 - - - +
63G PHE* 1.3 60.7 + - - +
71G SER* 5.0 0.4 - - - -
72G TYR 3.3 7.4 - - - -
73G LEU* 4.3 3.8 - - - -
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Residues in contact with PHE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ASN* 4.2 1.5 - - - -
53G GLY* 3.2 25.8 - - - -
54G LEU* 3.7 10.7 - - + +
62G SER* 1.3 74.7 - - - +
64G LEU* 1.3 72.0 + - - +
65G SER* 3.7 22.4 - - - -
68G LYS* 5.5 4.9 - - - -
70G TYR* 3.5 31.2 - + - -
71G SER* 2.8 30.3 + - - -
72G TYR* 2.9 57.7 + + + -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G TYR* 3.8 26.9 - - + +
29G PHE* 3.7 17.3 - - + -
32G LEU* 4.7 3.8 - - + -
49G ASN* 3.6 17.3 - - + +
50G VAL* 3.5 45.3 - - - +
51G LEU 3.5 11.7 - - - +
52G ASP* 3.5 5.5 - - - +
53G GLY 2.9 26.7 + - - -
63G PHE* 1.3 85.6 - - - +
65G SER* 1.3 71.3 + - - +
66G ARG* 4.3 3.8 - - + +
70G TYR 3.6 13.5 - - - +
71G SER* 4.3 7.6 - - - -
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G TYR* 3.9 1.2 + - - -
52G ASP* 3.5 3.5 - - - -
63G PHE* 3.7 21.4 - - - -
64G LEU* 1.3 77.0 - - - +
66G ARG* 1.3 57.9 + - - +
67G SER* 3.7 6.4 + - - -
68G LYS* 3.1 38.2 + - - +
69G GLY* 2.9 23.2 + - - -
70G TYR* 2.9 25.1 + - - +
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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