Contacts of the strand formed by residues 161 - 166 (chain s) 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 161 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17s LEU* 6.1 3.4 - - + -
18s LYS 3.5 9.2 - - - +
19s THR* 4.4 4.3 - - - +
49s TYR* 3.3 28.7 - - + +
50s ASP* 3.6 1.9 - - - +
51s ASN* 3.4 22.5 + - - -
52s THR* 3.2 12.3 + - - +
160s LYS* 1.3 72.1 - - - +
162s LYS* 1.3 62.4 - - - +
163s SER 4.9 7.2 - - - +
164s CYS* 6.4 0.7 - - + -
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Residues in contact with LYS 162 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18s LYS* 2.7 20.5 + - + +
19s THR* 5.3 3.6 - - - -
20s THR 5.8 0.2 - - - +
50s ASP* 4.8 10.5 - - - +
160s LYS 3.6 4.2 + - - +
161s ILE* 1.3 73.2 - - - +
163s SER* 1.3 60.7 + - - +
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Residues in contact with SER 163 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17s LEU* 3.7 2.3 - - - +
18s LYS* 3.1 36.1 + - - +
50s ASP* 6.1 2.0 - - - +
161s ILE* 3.6 5.9 - - - +
162s LYS* 1.3 79.6 + - - +
164s CYS* 1.3 65.2 + - - +
165s GLU* 4.2 1.3 - - - -
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Residues in contact with CYS 164 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16s LEU 3.4 8.7 - - - +
17s LEU* 5.0 5.2 - - + -
44s CYS* 3.6 41.2 - - + +
47s ALA* 5.8 5.0 - - - +
49s TYR* 5.4 13.0 - - + +
163s SER* 1.3 77.4 - - - +
165s GLU* 1.3 62.5 + - - +
166s VAL* 4.2 0.3 + - - +
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Residues in contact with GLU 165 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15s VAL* 3.3 7.8 - - - +
16s LEU* 2.8 47.6 + - + +
44s CYS* 5.4 2.0 - - - +
163s SER* 4.2 2.3 - - - -
164s CYS* 1.3 76.1 - - - +
166s VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 166 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14s LYS 4.4 0.4 - - - -
15s VAL* 4.3 8.3 - - + +
41s ILE* 6.0 4.5 - - + +
44s CYS* 5.8 7.0 - - + -
45s LEU* 5.9 8.5 - - + -
164s CYS 4.2 0.6 + - - +
165s GLU* 1.3 75.4 - - - +
167s LEU* 1.3 63.7 + - - +
168s PHE 3.6 8.5 - - - +
169s ASN* 5.0 11.8 - - + +
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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