Contacts of the strand formed by residues 67 - 72 (chain G) 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 ILE 67 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.4 21.7 - - - +
67A LYS* 3.7 4.7 - - - +
19G LEU* 4.9 2.7 - - + -
20G LYS 4.0 5.2 - - - +
21G LEU* 3.9 8.1 - - + -
38G MET* 3.5 36.6 - - + +
40G LEU* 3.5 37.2 - - + -
62G ILE* 3.5 34.5 - - + -
63G ARG 3.7 5.6 - - - +
64G GLY* 3.2 7.9 + - - +
66G SER* 1.3 79.1 - - - +
68G ILE* 1.3 63.8 + - - +
69G MET 4.3 15.3 - - - +
70G LEU* 5.0 5.6 - - + +
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Residues in contact with ILE 68 (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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22A THR* 4.5 13.2 - - + -
23A ASN* 6.1 1.8 - - + -
24A THR* 3.6 39.3 - - + +
28A TYR* 5.7 0.2 - - - +
63A ILE* 3.6 5.5 - - - +
64A ARG* 3.1 26.3 + - - +
67A LYS* 3.9 33.8 - - + +
20G LYS* 2.9 25.1 + - + +
21G LEU 3.7 26.5 - - - +
22G ASN* 4.3 9.9 - - - +
66G SER 4.7 0.7 - - - +
67G ILE* 1.3 75.7 - - - +
69G MET* 1.3 68.8 + - + +
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Residues in contact with MET 69 (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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28A TYR* 3.5 40.2 - - + +
58A LEU* 4.8 5.4 - - - -
61A VAL* 4.5 12.3 - - + -
62A TYR 3.3 12.8 - - - +
63A ILE* 4.5 14.4 - - + -
18G SER* 4.2 8.5 - - - +
19G LEU* 3.7 1.9 - - - +
20G LYS* 2.8 56.5 + - + +
26G HIS* 5.6 2.7 - - + -
67G ILE* 4.6 4.8 - - - +
68G ILE* 1.3 88.2 - - + +
70G LEU* 1.3 75.8 - - - +
71G GLU* 4.3 9.0 - - + +
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Residues in contact with LEU 70 (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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61A VAL* 3.3 6.1 - - - +
62A TYR* 2.9 62.2 + - + +
9G LEU* 4.1 17.7 - - + -
12G PHE* 4.0 25.6 - - + -
17G LEU* 4.1 13.9 - - + -
18G SER 3.4 4.5 - - - -
19G LEU* 3.2 24.5 - - + -
31G LEU* 5.4 0.9 - - + -
38G MET* 5.0 7.2 - - + -
40G LEU* 4.0 27.6 - - + -
67G ILE* 5.0 4.7 - - + +
69G MET* 1.3 77.2 - - - +
71G GLU* 1.3 58.0 + - - +
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Residues in contact with GLU 71 (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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58A LEU* 3.4 40.9 - - + +
59A GLU 5.3 1.8 + - - +
60A GLN 3.4 10.8 - - - +
61A VAL* 4.4 6.1 - - + +
17G LEU* 3.3 5.8 - - - -
18G SER* 2.7 55.5 + - - +
69G MET* 4.6 9.7 - - + +
70G LEU* 1.3 74.5 - - - +
72G ALA* 1.3 72.2 + - - +
73G LEU* 3.5 21.4 + - - +
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Residues in contact with ALA 72 (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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59A GLU* 4.7 7.8 - - - +
60A GLN* 2.9 25.4 + - + +
12G PHE* 3.9 15.7 - - + -
15G LYS* 5.5 0.9 - - + -
16G LYS 4.6 0.7 - - - +
17G LEU* 3.7 11.2 - - + +
70G LEU 4.3 0.2 - - - -
71G GLU* 1.3 81.4 - - - +
73G LEU* 1.3 61.8 + - - +
74G GLU 3.7 16.6 - - - +
76G VAL* 3.8 23.6 - - + -
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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