Contacts of the strand formed by residues 66 - 70 (chain A) in PDB entry 1FS6
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.8 31.2 - - + -
29A PRO* 4.8 1.8 - - + -
35A PHE* 3.1 17.9 - - + +
37A LEU* 4.1 14.6 - - + -
62A SER 4.1 4.0 - - - +
63A PHE* 3.2 38.8 + - + +
65A HIS* 1.3 81.4 - - - +
67A VAL* 1.3 65.4 + - - +
68A THR* 4.0 20.9 - - + -
99A ILE* 3.4 11.4 - - + +
103A ASN* 3.1 20.0 + - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PRO* 3.7 18.6 - - + -
35A PHE 2.8 8.2 + - - +
36A VAL* 3.1 11.6 - - + +
37A LEU* 2.7 32.6 + - - +
66A VAL* 1.3 74.4 - - - +
68A THR* 1.3 56.4 + - - +
69A PHE* 3.8 11.4 - - + -
103A ASN* 3.2 21.5 - - - +
105A ASN* 3.5 25.6 - - - +
128A TYR* 3.6 44.9 - - + +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.1 13.9 - - + -
39A LEU* 3.7 27.4 - - + -
66A VAL* 4.0 13.0 - - + -
67A VAL* 1.3 78.2 - - - +
69A PHE* 1.3 62.6 + - - +
70A ASN* 4.7 1.7 + - - -
93A PHE* 5.0 3.6 - - + -
94A PHE* 3.8 18.3 - - + -
99A ILE* 3.7 18.2 - - + +
103A ASN 2.8 7.7 + - - -
104A ILE* 3.7 14.9 - - - -
105A ASN* 2.8 34.1 + - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 3.6 31.0 - - + -
37A LEU 2.9 7.7 + - - +
38A GLY* 3.3 4.0 - - - -
39A LEU 2.8 23.1 + - - -
67A VAL* 3.8 13.2 - - + -
68A THR* 1.3 73.7 - - - +
70A ASN* 1.3 63.5 + - - +
105A ASN* 3.3 37.9 - - + -
121A TYR* 3.8 20.4 - + + +
124A LYS* 3.8 14.1 - - + -
125A ILE* 3.4 48.0 - - + -
128A TYR* 3.8 17.3 - + - -
131A ILE* 4.5 15.9 - - + -
134A PHE* 4.4 4.2 - - + -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.4 21.8 + - - +
40A PRO* 4.4 0.4 - - - +
41A THR* 3.6 13.3 - - - +
68A THR* 4.7 1.7 + - - -
69A PHE* 1.3 75.6 - - - +
71A MET* 1.3 63.9 + - - +
72A ASP 3.4 7.3 + - - +
89A MET* 3.2 47.3 - - - +
94A PHE* 4.2 8.0 - - - -
105A ASN 3.1 7.8 + - - +
106A LEU* 3.5 29.6 - - + +
107A LEU* 4.4 2.6 + - - +
121A TYR* 2.6 34.7 + - - +
134A PHE* 4.9 1.1 - - - -
188A VAL* 3.9 1.2 - - - +
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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