Contacts of the strand formed by residues 104 - 109 (chain D) in PDB entry 1FYR
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 ASP 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D SER* 5.7 0.6 - - - -
100D LYS* 3.7 6.4 - - - +
101D PHE* 3.0 33.1 + - - +
103D ASN* 1.3 95.2 + - - +
105D VAL* 1.3 74.9 + - - +
106D GLN* 5.2 9.9 + - + +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLU* 3.9 42.8 - - + +
74D LEU* 3.7 33.4 - - + -
75D SER* 3.8 33.9 - - - +
99D VAL 3.3 7.0 - - - +
100D LYS* 4.6 2.0 - - - -
104D ASP* 1.3 83.9 - - - +
106D GLN* 1.3 71.6 + - - +
107D HIS* 4.1 14.7 - - + -
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Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C SER* 4.9 0.3 + - - -
144C GLN* 3.0 28.8 + - - +
146C ILE* 3.5 9.3 - - - +
98D SER* 3.2 3.3 - - - -
99D VAL* 2.6 47.9 + - + +
101D PHE* 3.2 31.4 + - + +
104D ASP* 4.2 8.4 + - + -
105D VAL* 1.3 78.8 - - - +
107D HIS* 1.3 63.2 + - - +
108D PHE* 3.5 31.7 - - + -
1L VAL* 3.6 17.6 - - + +
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Residues in contact with HIS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG* 3.3 61.3 - - + +
70D ALA* 4.5 0.7 - - + -
71D GLU* 2.7 42.0 + - + +
86D ARG* 3.2 7.9 + - - +
96D SER* 5.9 0.2 - - - -
97D LEU 3.2 4.9 - - - +
98D SER* 2.6 35.4 + - - -
105D VAL* 4.1 9.5 - - + +
106D GLN* 1.3 75.3 - - - +
108D PHE* 1.3 56.3 + - - +
-1L ACE 3.9 3.7 + - - +
0L PTR 3.2 11.1 - - + -
1L VAL* 2.7 35.2 + - - +
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Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C VAL* 3.4 37.2 - - + -
141C SER* 3.7 19.7 - - - -
146C ILE* 4.3 0.9 - - + -
96D SER* 3.5 2.3 - - - -
97D LEU* 2.7 50.2 + - + +
99D VAL* 3.5 32.5 - - + -
106D GLN* 3.5 30.3 - - + -
107D HIS* 1.3 77.2 - - - +
109D LYS* 1.3 61.1 - - - +
120D LEU* 4.2 12.8 - - + -
0L PTR 3.7 3.1 - - - -
1L VAL* 3.5 25.6 - - + -
2L ASN* 3.6 24.9 - - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D SER* 3.8 11.0 - - - -
90D SER* 4.6 1.0 + - - -
91D ALA* 3.8 20.3 - - - +
94D ASP* 4.1 13.2 + - + -
95D PHE 3.3 16.6 - - - +
96D SER* 3.7 17.3 - - - -
108D PHE* 1.3 74.3 - - - +
110D VAL* 1.3 73.7 + - - +
111D LEU* 3.3 14.2 + - + +
120D LEU* 3.9 4.0 - - - +
0L PTR 3.5 30.3 - - + -
2L ASN* 2.8 34.2 + - - +
3L VAL* 3.9 18.9 - - + +
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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