Contacts of the strand formed by residues 17 - 22 (chain e) 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 17 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B ASP* 5.8 2.6 - - + +
15e GLY 4.3 0.4 + - - -
16e HIS* 1.3 75.7 - - - +
18e VAL* 1.3 61.2 + - - +
30e GLY* 3.4 13.5 - - - +
31e LYS* 4.4 1.9 - - + +
72e ILE 4.7 0.2 - - - +
73e LEU 4.9 0.2 - - - -
74e PRO* 4.0 23.6 - - - +
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Residues in contact with VAL 18 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13e ALA* 5.9 6.1 - - + -
16e HIS 4.4 4.9 - - - +
17e ILE* 1.3 75.9 - - - +
19e THR* 1.3 64.5 + - - +
28e TYR 3.8 0.7 - - - +
29e ARG* 3.4 3.4 - - - +
30e GLY 3.0 30.6 + - - +
32e LEU* 5.1 10.1 - - + -
71e LEU* 5.9 3.4 - - + -
72e ILE 3.5 15.3 - - - +
73e LEU* 4.9 4.3 - - + -
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Residues in contact with THR 19 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18e VAL* 1.3 76.9 - - - +
20e CYS* 1.3 61.6 + - - +
21e GLU 4.2 0.9 - - - -
27e VAL* 6.3 2.7 - - - -
28e TYR 3.0 7.6 - - - -
29e ARG* 4.2 8.3 - - - +
71e LEU* 3.4 8.8 - - - +
72e ILE* 3.1 45.6 + - - +
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Residues in contact with CYS 20 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19e THR* 1.3 70.8 - - - +
21e GLU* 1.3 59.5 + - - +
22e THR 3.7 0.5 + - - -
26e GLU 3.1 5.0 - - - +
27e VAL* 4.4 0.7 - - - -
28e TYR* 2.4 60.1 + - + +
63e ILE* 5.4 12.3 - - + -
68e ILE* 6.0 5.2 - - + -
70e PHE 4.0 7.0 - - - +
71e LEU* 5.6 2.5 - - + -
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Residues in contact with GLU 21 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19e THR* 4.2 1.4 - - - -
20e CYS* 1.3 70.3 - - - +
22e THR* 1.3 64.1 + - - +
25e GLY* 5.7 2.9 - - - -
26e GLU 3.3 8.1 - - - +
27e VAL* 4.3 8.1 - - + +
68e ILE* 4.0 1.6 - - - -
69e ARG* 2.9 30.1 + - + +
70e PHE* 3.5 14.8 + - + +
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Residues in contact with THR 22 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20e CYS 3.7 2.0 + - - -
21e GLU* 1.3 78.6 - - - +
23e ASN* 1.3 65.6 + - - +
24e THR* 3.2 10.3 + - - -
25e GLY* 3.4 9.8 + - - -
26e GLU* 2.9 28.8 + - - -
67e LYS* 3.1 21.5 - - - -
68e ILE* 4.6 0.2 - - - +
69e ARG* 3.4 10.1 - - - +
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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