Contacts of the strand formed by residues 65 - 69 (chain n) in PDB entry 6FF7
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 65 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102h ARG* 3.6 19.1 - - + +
17n ILE* 6.0 5.2 - - + -
18n GLU 4.2 3.4 - - - +
19n LEU* 4.5 1.6 - - - +
20n LYS* 4.4 2.2 - - - +
36n MET* 5.8 2.5 - - + +
61n ARG 4.2 1.4 + - - +
62n GLY* 3.2 16.8 + - - +
63n ASN 3.7 8.5 - - - +
64n ASN* 1.3 79.0 - - - +
66n ARG* 1.3 64.7 + - - +
67n TYR* 4.8 4.0 - - - +
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Residues in contact with ARG 66 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48h ASN* 6.2 4.3 - - + -
101h LEU* 3.8 0.9 - - - +
102h ARG* 2.8 32.3 + - - +
105h SER* 4.9 15.5 - - - -
18n GLU* 2.8 24.0 + - + +
19n LEU 3.9 15.5 - - - +
20n LYS* 3.9 6.0 - - + +
64n ASN 3.7 2.4 + - - -
65n ILE* 1.3 73.3 - - - +
67n TYR* 1.3 62.9 + - + +
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Residues in contact with TYR 67 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329 ASP* 6.0 4.3 - - + -
3389 ARG* 5.1 9.0 - - + -
100h PHE 2.9 18.8 - - - +
101h LEU* 3.7 11.2 - - + +
102h ARG* 4.4 0.9 - - - +
17n ILE* 3.3 4.2 - - - +
18n GLU* 2.8 36.4 + - + +
65n ILE* 3.8 4.6 - - - +
66n ARG* 1.3 84.8 - - + +
68n PHE* 1.3 60.8 + - - +
69n ILE 4.1 0.3 + - - -
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Residues in contact with PHE 68 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259 GLN* 4.9 11.0 - - + -
1279 LEU* 1.4 156.1 - - + +
1289 VAL 4.1 1.1 - - - +
1329 ASP* 6.4 0.2 - - - -
99h MET* 3.1 6.7 - - - +
100h PHE* 2.6 52.2 + - + +
17n ILE* 4.4 3.8 - - + +
67n TYR* 1.3 74.3 - - - +
69n ILE* 1.3 52.5 + - - +
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Residues in contact with ILE 69 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269 ASN 1.2 31.8 - - - +
1279 LEU* 1.8 35.4 + - - +
1309 PHE* 1.2 63.0 + - + +
1319 THR* 2.8 24.2 - - - +
1329 ASP* 3.8 1.8 - - - +
98h LYS 3.9 4.7 - - - +
99h MET* 4.1 2.9 - - + -
16n THR 2.6 0.8 + - - -
67n TYR 4.1 0.6 + - - -
68n PHE 1.3 64.0 - - - -
70n LEU* 1.3 50.9 - - - +
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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