Contacts of the strand formed by residues 34 - 39 (chain H) in PDB entry 5A15
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 GLN 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G PHE* 5.6 8.1 - - - -
30H ASN* 4.5 0.2 - - - -
31H VAL 2.8 35.7 + - - +
32H GLY 3.4 1.4 - - - +
33H GLY* 1.3 83.9 - - - +
35H VAL* 1.3 65.6 + - - +
36H TYR* 3.5 19.5 - - + +
79H GLY* 3.6 27.6 - - - +
80H PHE* 3.7 34.1 - - + +
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Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLY 4.8 3.1 - - - +
33G GLY* 5.7 1.0 - - - -
28H GLU* 4.4 10.3 - - + +
29H LEU 3.3 12.8 - - - +
30H ASN* 5.1 4.7 - - - -
33H GLY 3.9 6.7 + - - +
34H GLN* 1.3 76.0 - - - +
36H TYR* 1.3 73.9 + - - +
37H PHE* 3.8 28.0 - - + -
72H ARG* 3.5 30.5 - - - +
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Residues in contact with TYR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLY 4.3 9.9 - - - -
80G PHE* 6.0 5.6 - + - -
27H VAL 3.7 0.3 - - - +
28H GLU* 3.6 1.2 - - - -
29H LEU* 2.6 52.3 + - + +
31H VAL* 4.1 4.7 - - + -
34H GLN* 3.5 32.3 - - + +
35H VAL* 1.3 75.2 - - - +
37H PHE* 1.3 64.1 + - - +
79H GLY 2.6 30.6 + - - -
80H PHE* 3.9 2.1 + - - -
82H PHE* 3.6 24.7 - + + -
83H ARG* 3.2 43.7 + - + +
86H LEU* 3.9 24.9 - - + -
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Residues in contact with PHE 37 (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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30G ASN* 3.8 20.0 - - - -
32G GLY* 3.5 8.8 + - - -
33G GLY* 3.3 30.3 - - - +
68G ASP* 4.9 7.4 - - + -
69G SER* 5.4 5.6 - - - -
72G ARG* 5.3 6.7 - - - -
74G PHE* 3.4 25.4 - - + -
26H VAL* 4.2 18.4 - - + -
27H VAL 3.4 3.4 - - - -
28H GLU* 3.2 50.7 - - + -
35H VAL* 3.8 14.1 - - + -
36H TYR* 1.3 78.8 - - - +
38H THR* 1.3 63.5 + - - +
86H LEU* 4.1 2.8 - - - +
90H ARG* 3.5 14.2 + - - -
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Residues in contact with THR 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G PHE* 3.6 9.1 - - - -
76G ASP* 3.2 17.9 + - - -
26H VAL* 3.3 8.2 - - - +
27H VAL 2.7 33.4 + - - +
29H LEU* 4.2 9.9 - - + -
37H PHE* 1.3 78.2 - - - +
39H ARG* 1.3 70.6 + - - +
42H THR* 3.3 16.1 - - - +
43H LEU* 3.6 36.8 - - + -
86H LEU* 3.7 17.1 - - + +
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Residues in contact with ARG 39 (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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65G LEU 4.8 5.9 - - - +
66G ALA* 3.7 34.4 - - + +
74G PHE* 4.0 15.4 + - + -
76G ASP* 3.1 34.9 - - + +
25H GLU* 3.4 20.9 + - + +
26H VAL* 4.4 1.3 - - - +
38H THR* 1.3 84.4 + - - +
40H HIS* 1.3 64.6 + - - +
41H SER* 3.5 23.0 + - - +
42H THR* 3.0 20.2 + - - +
43H LEU* 3.5 3.8 + - - +
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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
------------------------------------------------------------
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