Contacts of the strand formed by residues 108 - 115 (chain F) in PDB entry 6XXD
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 GLY 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ILE* 4.2 21.3 - - - -
22B PRO 5.4 1.1 + - - -
24B LEU* 6.1 1.3 - - - -
70E LYS* 5.6 0.9 - - - -
44F VAL* 5.6 2.2 - - - -
103F ALA* 3.5 0.4 - - - -
104F THR 2.9 35.5 + - - -
105F PRO 3.9 4.3 + - - -
106F ASP 3.5 2.4 - - - -
107F LYS* 1.3 80.9 - - - +
109F VAL* 1.3 61.7 + - - -
110F TYR* 3.4 9.9 - - - -
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA* 4.7 9.3 + - + +
18B ALA* 4.6 17.8 - - - +
21B ILE* 4.9 8.2 - - + +
37F THR* 4.3 24.1 - - + +
40F LEU* 3.8 39.0 - - + +
41F ASN* 4.0 10.5 - - + +
44F VAL* 3.9 27.4 - - + -
101F PHE* 4.8 4.5 - - + -
102F ALA 3.6 13.0 - - - +
103F ALA* 4.1 3.1 - - + -
107F LYS 4.8 1.3 - - - +
108F GLY* 1.3 70.7 - - - -
110F TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F PHE* 3.4 9.5 - - - +
102F ALA* 2.8 52.1 + - + +
104F THR* 4.2 9.3 - - + +
107F LYS* 3.5 53.3 + - + +
108F GLY 3.4 15.3 - - - -
109F VAL* 1.3 73.9 - - - +
111F LYS* 1.3 71.1 + - - +
112F THR* 5.2 0.9 - - - -
124F CYS* 3.7 7.3 - - - +
125F PRO* 2.7 49.9 + - + +
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Residues in contact with LYS 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.7 28.0 + - - +
53A ASP* 3.9 24.5 + - - +
30F ARG* 5.2 2.2 - - - +
98F THR* 5.7 0.4 - - - +
99F VAL* 4.0 23.3 - - + -
100F TRP 3.7 4.3 - - - +
101F PHE* 3.7 28.2 - - + -
110F TYR* 1.3 86.8 - - - +
112F THR* 1.3 61.4 + - - +
113F ASN* 5.1 1.4 - - - +
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Residues in contact with THR 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ILE* 6.0 1.8 - - + -
99F VAL* 3.4 23.6 - - - +
100F TRP* 3.0 41.8 + - + +
101F PHE* 4.8 1.1 - - - +
102F ALA* 5.3 5.6 - - + +
110F TYR* 4.2 2.8 + - - -
111F LYS* 1.3 74.2 - - - +
113F ASN* 1.3 73.5 + - - +
114F THR* 3.8 20.4 + - - +
121F PRO* 4.2 8.8 - - + +
125F PRO* 3.6 32.9 - - + +
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Residues in contact with ASN 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F VAL* 4.2 7.0 - - - +
111F LYS 5.1 1.4 - - - +
112F THR* 1.3 82.6 + - - +
114F THR* 1.3 62.1 + - - +
115F ALA* 3.5 2.9 + - - +
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Residues in contact with THR 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F VAL* 3.3 7.7 - - - +
100F TRP* 3.2 29.3 + - + +
112F THR* 3.3 9.5 + - - +
113F ASN* 1.3 77.3 - - - +
115F ALA* 1.3 66.6 + - - +
118F SER* 4.2 9.2 - - - -
119F SER 3.5 25.4 - - - +
121F PRO* 3.8 25.6 - - + +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F THR 4.0 11.7 - - - +
99F VAL* 4.2 3.6 - - + -
100F TRP* 2.9 17.5 + - - -
113F ASN 3.5 3.7 + - - +
114F THR* 1.3 75.7 - - - +
116F VAL* 1.3 63.5 + - + +
117F THR* 3.3 17.5 - - - +
118F SER* 3.2 24.1 + - - +
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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