Contacts of the strand formed by residues 88 - 94 (chain F) in PDB entry 6BA5
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 ALA 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F ARG* 4.0 11.2 - - + -
38F GLN 3.4 28.7 - - - +
39F ALA* 3.8 3.6 - - + +
40F PRO* 4.3 4.3 - - - -
86F ASP 3.2 4.3 + - - +
87F THR* 1.3 78.6 - - - +
89F THR* 1.4 60.9 - - - +
90F TYR* 3.3 24.9 - - + -
111F LEU* 3.9 6.5 - - - -
112F VAL 2.9 28.5 + - - +
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Residues in contact with THR 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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37F ARG* 3.2 4.0 - - - -
38F GLN* 2.9 36.7 + - - -
40F PRO* 5.5 0.2 - - - +
88F ALA* 1.4 70.9 - - - +
90F TYR* 1.3 60.8 + - - +
91F PHE* 3.7 24.9 - - + -
108F PRO 4.9 0.9 - - - +
109F GLY* 3.7 27.4 - - - -
110F THR 3.4 11.9 - - - +
111F LEU* 3.9 17.8 - - - +
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Residues in contact with TYR 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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7D GLU* 2.6 22.8 - - - +
19F LEU* 3.4 23.3 - - + -
35F TRP* 4.8 4.0 - + + -
36F VAL 3.6 2.0 - - - -
37F ARG* 3.1 39.6 + - + -
47F ILE* 3.7 18.4 - - + -
66F PHE* 3.6 25.0 - + - -
77F LEU* 3.9 10.5 - - + -
79F MET* 3.9 8.0 - - + -
86F ASP* 2.7 33.9 + - - +
88F ALA* 3.3 21.5 - - + -
89F THR* 1.3 72.0 - - - +
91F PHE* 1.3 57.0 + - - +
109F GLY* 3.3 0.7 - - - -
110F THR 2.9 20.7 + - - +
112F VAL* 3.7 24.0 - - + -
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Residues in contact with PHE 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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7D GLU* 3.9 4.0 - - - -
39E GLN* 4.1 12.8 - - - -
43E GLN 4.5 2.5 - - - -
44E PRO* 3.7 24.5 - - + -
45E PRO* 4.9 0.4 - - + -
35F TRP* 3.3 11.1 - - - -
36F VAL* 2.7 49.3 + - + +
37F ARG* 4.8 0.7 - - - -
38F GLN* 3.8 27.8 - - + -
44F LEU* 4.6 3.8 - - + -
89F THR* 3.7 27.6 - - + -
90F TYR* 1.3 75.0 - - - +
92F CYS* 1.3 60.7 + - - +
106F TRP* 3.7 27.4 - + + -
107F GLY 3.4 18.8 - - - +
108F PRO 3.6 18.2 - - - -
109F GLY* 3.6 8.1 - - - -
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Residues in contact with CYS 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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5D GLU* 3.2 23.1 - - + -
7D GLU* 3.8 3.0 + - - -
21F CYS* 2.1 50.9 - - + -
33F ILE* 4.0 7.6 - - + -
34F SER 3.3 8.5 - - - +
35F TRP* 3.9 15.0 - - + -
91F PHE* 1.3 74.7 - - - +
93F ALA* 1.3 61.7 + - - +
106F TRP* 3.4 5.2 - - - +
107F GLY* 2.8 34.6 + - - +
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Residues in contact with ALA 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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5D GLU* 5.4 0.9 - - - -
33F ILE* 3.5 7.2 - - - -
34F SER* 2.9 36.2 + - - +
36F VAL* 5.1 2.0 - - + -
92F CYS* 1.3 77.2 - - - +
94F ARG* 1.3 61.4 + - - +
95F GLY 3.9 0.3 - - - +
103F PHE* 4.0 22.2 - - + -
105F ILE 3.2 8.5 - - - +
106F TRP* 3.7 33.9 - - + +
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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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3D VAL 3.8 15.0 - - - +
4D LYS 5.6 1.2 + - - -
5D GLU* 4.7 6.0 + - - +
23F ALA* 5.7 2.8 - - - +
26F SER* 3.3 23.4 + - - -
31F TYR* 3.5 61.5 + - + -
32F PRO 3.7 7.9 - - - +
33F ILE* 3.8 7.7 - - + +
93F ALA* 1.3 72.2 - - - +
95F GLY* 1.3 58.4 - - - +
102F ASP 3.8 0.2 - - - -
103F PHE* 2.7 33.3 + - - -
104F ASN* 3.7 30.4 - - - +
105F ILE* 2.9 37.9 + - + +
329O LYS* 5.9 6.3 - - - +
381O PHE* 4.3 10.5 - - + -
384O ASP* 4.4 7.9 + - - -
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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