Contacts of the strand formed by residues 52 - 56 (chain H) in PDB entry 3QSU
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 52 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLU* 5.0 11.0 - - - +
38H GLU* 5.7 2.4 + - - -
45H SER* 4.7 10.3 - - - -
46H LEU 4.0 3.8 - - - +
47H ASN* 4.7 5.8 - - - +
51H LYS* 1.3 69.6 - - - +
53H HIS* 1.3 70.7 + - - +
54H LEU* 4.1 14.8 + - + +
10I LYS* 4.3 18.6 - - - +
11I ALA* 5.4 2.8 - - - +
15I PHE* 5.5 10.0 - - + -
63I TYR 3.8 0.7 - - - +
64I THR* 3.5 3.5 - - - +
65I VAL* 3.2 39.7 + - + +
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Residues in contact with HIS 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H MET* 3.2 31.4 - - + -
44H VAL 3.6 1.6 - - - +
45H SER* 3.4 3.8 - - - -
46H LEU* 2.7 47.9 + - + +
48H SER* 3.0 29.0 + - - -
49H GLN 4.5 0.7 - - - -
51H LYS* 3.0 30.6 + - + -
52H GLN* 1.3 76.6 + - - +
54H LEU* 1.3 60.1 + - - +
55H ILE* 3.8 8.2 + - + +
78H ZN 2.4 31.8 - - - -
62I THR* 3.6 13.7 - - + -
63I TYR 3.4 4.3 - - - -
64I THR* 4.2 10.5 - - + -
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Residues in contact with LEU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H VAL* 4.5 15.7 - - + -
44H VAL 3.7 1.6 - - - -
45H SER* 4.2 12.3 - - - +
52H GLN* 4.1 9.8 + - + +
53H HIS* 1.3 70.9 - - - +
55H ILE* 1.3 61.4 + - - +
56H TYR 4.2 0.2 + - - -
7I ILE* 3.8 29.4 - - + +
8I GLN* 4.4 11.2 - - + -
10I LYS* 4.3 3.1 - - - +
11I ALA* 3.8 28.3 - - + -
12I LEU* 4.3 7.9 - - + -
15I PHE* 5.0 5.2 - - + -
61I SER 4.2 0.2 - - - +
62I THR* 3.4 1.9 - - - -
63I TYR* 2.8 77.0 + - + +
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Residues in contact with ILE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 4.9 11.2 - - + -
26H PHE* 3.7 33.4 - - + -
32H MET* 4.2 4.3 - - - -
43H VAL* 3.0 8.7 - - - -
44H VAL* 2.7 48.6 + - + +
46H LEU* 4.1 34.8 - - + -
53H HIS* 4.3 3.4 - - + +
54H LEU* 1.3 75.7 - - - +
56H TYR* 1.3 75.3 + - - +
59H ALA* 4.9 0.2 - - + -
60H ILE* 3.8 17.3 - - + -
61I SER 3.6 10.5 - - - +
62I THR* 3.8 17.9 - - + +
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H TYR* 3.5 8.7 - - + -
43H VAL* 3.5 14.6 - - + -
55H ILE* 1.3 86.3 - - - +
57H LYS* 1.3 64.6 + - - +
58H HIS* 3.3 34.1 - + + +
59H ALA* 3.0 12.6 + - - +
60H ILE* 3.6 2.0 - - - +
79H ZN 4.7 3.6 - - - -
8I GLN* 2.5 41.4 + - - +
57I LYS* 3.0 20.6 - - + +
60I ILE* 3.5 31.9 - - + -
61I SER 3.0 12.2 + - - +
63I TYR* 2.9 46.2 + + - -
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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