Contacts of the strand formed by residues 88 - 94 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H ARG* 4.0 10.3 - - + -
38H GLN 3.4 29.4 - - - +
39H ALA* 3.8 4.5 - - + +
40H PRO* 4.3 4.0 - - - -
86H ASP 3.1 4.3 + - - +
87H THR* 1.3 79.0 - - - +
89H THR* 1.3 61.7 + - - +
90H TYR* 3.3 24.0 - - + -
111H LEU* 3.9 6.3 - - - -
112H VAL 2.9 29.1 + - - +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H ARG* 3.2 4.0 - - - -
38H GLN* 2.9 39.1 + - - -
88H ALA* 1.3 70.6 - - - +
90H TYR* 1.3 62.6 + - - +
91H PHE* 3.7 23.9 - - + -
108H PRO 4.9 0.9 - - - +
109H GLY* 3.7 27.4 - - - -
110H THR 3.4 11.9 - - - +
111H LEU* 3.7 20.0 - - - +
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Residues in contact with TYR 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU* 3.4 24.8 - - + +
35H TRP* 4.9 5.6 - - + -
36H VAL 3.6 2.0 - - - -
37H ARG* 3.1 44.7 + - + -
47H ILE* 3.7 19.1 - - + -
66H PHE* 3.9 6.0 - + - -
77H LEU* 3.9 5.2 - - + -
79H MET* 3.4 27.3 - - + -
86H ASP* 2.7 34.2 + - - +
88H ALA* 3.3 21.8 - - + -
89H THR* 1.3 74.1 - - - +
91H PHE* 1.3 61.6 + - - +
109H GLY* 3.3 2.1 - - - -
110H THR* 2.9 30.6 + - - +
112H VAL* 3.8 23.1 - - + -
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Residues in contact with PHE 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLN* 4.1 17.7 - - - -
43G GLN 4.4 2.7 - - - -
44G PRO* 3.6 25.4 - - + -
45G PRO* 4.9 0.7 - - + -
35H TRP* 3.4 11.4 - - - -
36H VAL* 2.8 48.6 + - + +
37H ARG* 4.8 0.9 - - - -
38H GLN* 3.9 22.0 - - + -
44H LEU* 4.6 3.8 - - + -
89H THR* 3.7 27.1 - - + -
90H TYR* 1.3 75.1 - - - +
92H CYS* 1.3 60.9 + - - +
106H TRP* 3.6 27.1 - + + -
107H GLY 3.5 19.1 - - - +
108H PRO 3.6 17.0 - - - -
109H GLY* 3.5 11.7 - - - +
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Residues in contact with CYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H CYS* 2.1 51.8 - - + -
33H ILE* 4.0 9.6 - - + -
34H SER 3.3 8.7 - - - +
35H TRP* 3.8 15.1 - - + -
91H PHE* 1.3 75.5 - - - +
93H ALA* 1.3 63.0 + - - +
106H TRP* 3.4 4.9 - - - +
107H GLY* 2.8 42.2 + - - +
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Residues in contact with ALA 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ILE* 3.5 8.1 - - - -
34H SER* 2.8 34.9 + - - +
36H VAL* 5.3 1.8 - - + -
92H CYS* 1.3 77.9 - - - +
94H ARG* 1.3 62.3 + - - +
95H GLY 3.8 0.5 - - - +
103H PHE* 4.0 22.0 - - + -
105H ILE 3.2 9.0 - - - +
106H TRP* 3.7 32.8 - - + +
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Residues in contact with ARG 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ALA* 5.8 3.4 - - - +
24H SER 5.9 1.0 + - - -
26H SER* 3.3 23.6 + - - -
31H TYR* 3.5 63.5 + - + -
32H PRO 3.7 3.8 - - - -
33H ILE* 3.8 8.6 - - + +
93H ALA* 1.3 72.0 - - - +
95H GLY* 1.3 59.7 + - - +
102H ASP* 3.8 0.8 - - - -
103H PHE* 2.7 33.8 + - - -
104H ASN* 3.7 30.0 - - - +
105H ILE* 2.9 43.8 + - + +
329P LYS* 5.9 6.9 - - - +
381P PHE* 4.4 9.2 - - + -
384P ASP* 4.5 7.1 + - - -
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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