Contacts of the strand formed by residues 87 - 94 (chain F) in PDB entry 4X6D
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 SER 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F ARG* 3.3 22.2 + - - +
37F GLN 3.4 6.3 + - - -
38F ASP* 3.2 22.6 + - - +
39F PRO* 6.4 0.9 - - - -
85F GLN 3.0 8.1 + - - -
86F THR* 1.3 77.5 - - - +
88F VAL* 1.3 84.4 + - - +
89F TYR* 3.9 9.7 - - - -
110F THR 3.7 1.0 - - - +
111F ARG* 3.9 3.1 - - - +
112F LEU* 3.0 32.2 + - - +
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Residues in contact with VAL 88 (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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40E ARG* 3.6 26.9 - - - +
36F ARG* 3.3 1.7 - - - -
37F GLN* 2.9 39.1 + - + +
39F PRO* 6.3 2.2 - - + -
87F SER* 1.3 83.9 + - - +
89F TYR* 1.3 63.8 - - - +
90F PHE* 3.5 31.8 - - + -
109F GLY* 4.5 1.8 - - - -
110F THR 3.3 17.3 - - - +
111F ARG* 3.7 19.5 - - + +
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Residues in contact with TYR 89 (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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6F GLN* 3.0 7.9 + - - -
21F LEU* 3.9 24.0 - - + -
34F TRP* 3.9 5.6 - - + -
35F TYR 3.3 5.4 - - - +
36F ARG* 3.9 8.3 - - + -
46F ILE* 3.8 22.2 - - + -
64F TYR* 2.6 46.4 + + - -
76F LEU* 3.9 11.0 - - + -
78F LEU* 5.2 2.0 - - + -
85F GLN* 2.7 30.0 + - - +
87F SER* 3.9 18.5 - - - -
88F VAL* 1.3 75.6 - - - +
90F PHE* 1.3 62.5 + - - +
109F GLY* 3.1 3.6 - - - -
110F THR* 2.8 46.5 + - - +
112F LEU* 3.8 21.5 - - + +
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Residues in contact with PHE 90 (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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37E GLN* 3.6 16.8 - - - -
40E ARG 6.3 0.4 - - - -
41E LYS 3.9 4.0 - - - -
42E GLY* 3.6 24.5 - - - -
43E PRO* 4.1 4.3 - - + -
6F GLN* 3.4 0.7 - - - -
33F TYR 3.8 0.3 - - - +
34F TRP* 3.4 5.5 - - - -
35F TYR* 2.6 48.2 + - + +
37F GLN* 3.5 31.9 - - + -
43F LEU* 4.3 7.9 - - + -
88F VAL* 3.5 33.4 - - + -
89F TYR* 1.3 74.0 - - - +
91F CYS* 1.3 61.9 - - - +
106F PHE* 3.9 20.0 - + + -
107F GLY 3.8 13.0 - - - -
108F GLN 3.8 4.0 - - - -
109F GLY* 3.5 22.9 - - - -
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Residues in contact with CYS 91 (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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4F VAL* 4.1 6.2 - - + +
6F GLN* 2.7 20.6 + - + +
23F CYS* 2.0 58.3 - - + -
32F MET* 4.4 2.7 - - - -
33F TYR 3.3 10.8 - - - +
34F TRP* 3.7 14.1 - - + -
74F PHE* 5.4 0.9 - - - -
90F PHE* 1.3 75.3 - - - +
92F ALA* 1.3 72.3 + - - +
106F PHE* 3.4 3.0 - - - -
107F GLY 2.7 25.3 + - - -
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Residues in contact with ALA 92 (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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4F VAL* 5.0 1.6 - - - -
32F MET* 3.2 4.7 - - - +
33F TYR* 2.7 49.8 + - + -
35F TYR* 4.2 6.5 - - + -
91F CYS* 1.3 81.9 - - - +
93F SER* 1.3 62.0 + - - +
104F ALA* 4.4 4.9 - - + -
105F PHE 3.0 13.9 - - - +
106F PHE* 3.8 29.6 - - + -
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Residues in contact with SER 93 (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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4F VAL* 3.6 19.5 - - - +
25F GLN* 3.8 13.9 - - - +
27F MET* 3.9 0.3 - - - +
29F HIS* 2.8 20.8 + - - -
31F TYR 3.2 15.3 - - - -
32F MET* 3.7 14.1 - - - -
33F TYR* 4.4 1.3 - - - -
92F ALA* 1.3 76.1 - - - +
94F ARG* 1.3 63.4 + - - +
104F ALA* 4.3 2.5 - - - -
105F PHE* 2.9 35.1 + - - -
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Residues in contact with ARG 94 (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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91E SER* 5.7 2.0 + - - -
94E LEU* 6.0 1.4 - - - +
96E ASN* 4.2 12.1 + - - +
98E GLY* 3.7 26.2 + - - -
29F HIS* 3.7 14.1 - - - +
31F TYR* 3.1 38.2 + - + +
33F TYR* 3.9 22.9 + - + +
93F SER* 1.3 80.8 + - - +
95F TYR* 1.3 96.0 + - - +
96F PHE 2.9 20.0 + - - -
98F PRO* 3.3 18.8 - - + +
102F MET* 4.2 20.4 - - - +
103F GLY 3.6 28.6 + - - +
104F ALA* 3.9 6.7 - - + -
105F PHE* 4.8 2.7 - - + -
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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