Contacts of the strand formed by residues 32 - 39 (chain H) in PDB entry 6X34
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 32 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25H ASN* 4.4 18.6 - - - +
26H ALA 4.6 2.9 - - - -
27H THR* 5.1 3.6 - - - +
28H VAL 4.9 1.1 - - - +
31H GLU* 1.3 78.8 - - - +
33H LEU* 1.3 58.0 + - - +
34H LYS 4.4 0.2 + - - -
53H SER* 4.9 5.7 + - - -
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Residues in contact with LEU 33 (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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25H ASN* 3.2 3.2 + - - +
26H ALA* 2.8 46.4 + - + +
28H VAL* 4.3 14.8 - - + -
31H GLU 3.4 1.3 + - - +
32H GLN* 1.3 74.4 - - - +
34H LYS* 1.3 61.7 + - - +
35H LEU 4.1 0.2 + - - -
51H PRO* 6.0 5.6 - - + -
53H SER* 4.3 4.9 - - - +
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Residues in contact with LYS 34 (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 GLN* 3.4 24.2 - - - +
24H CYS 3.3 13.9 - - - +
25H ASN* 4.2 11.7 - - + +
32H GLN 4.3 0.2 - - - -
33H LEU* 1.3 72.1 - - - +
35H LEU* 1.3 61.1 + - - +
51H PRO* 3.7 4.1 - - - +
52H THR* 3.3 18.2 + - - +
53H SER* 3.2 23.6 + - - +
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Residues in contact with LEU 35 (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 GLN* 3.4 22.5 - - - +
24H CYS* 3.2 16.9 + - + +
26H ALA* 5.4 4.8 - - + +
33H LEU 4.1 2.2 + - - -
34H LYS* 1.3 71.9 - - - +
36H CYS* 1.3 61.8 + - - +
49H LEU* 3.8 36.1 - - + -
50H GLU 3.2 12.8 - - - +
51H PRO* 3.7 7.9 - - + -
52H THR* 4.7 0.9 - - - -
182H LEU* 5.8 1.3 - - + -
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Residues in contact with CYS 36 (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 VAL* 3.7 20.9 - - - -
22H LEU 3.2 24.0 - - - -
23H GLN* 5.0 4.7 - - + +
35H LEU* 1.3 77.2 - - - +
37H LEU* 1.3 72.3 + - - +
38H ALA* 6.1 0.2 - - + -
49H LEU* 3.3 4.6 - - - -
50H GLU* 2.5 50.8 + - + +
52H THR* 4.6 14.8 - - + -
65H CYS* 4.4 14.1 - - - -
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Residues in contact with LEU 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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22H LEU* 4.2 19.8 + - + +
36H CYS* 1.3 77.5 - - - +
38H ALA* 1.3 63.3 + - - +
39H ALA* 4.7 1.1 - - + +
47H CYS* 3.8 35.7 - - + -
48H PHE 3.5 9.6 - - - +
49H LEU* 4.5 2.6 - - - +
65H CYS* 3.4 19.1 - - - +
67H PHE* 3.9 31.7 - - + -
109H LEU* 6.3 3.1 - - + -
135H VAL* 5.0 5.4 - - + -
191H VAL* 4.3 31.2 - - + -
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Residues in contact with ALA 38 (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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36H CYS* 3.6 4.9 + - + +
37H LEU* 1.3 78.6 - - - +
39H ALA* 1.3 61.2 + - - +
40H GLU 4.3 0.2 + - - -
47H CYS* 3.3 3.8 - - - +
48H PHE* 3.0 49.3 + - + +
50H GLU* 4.9 7.6 - - + -
61H ASP 5.6 0.4 - - - +
64H ILE* 4.5 21.1 - - + -
65H CYS* 4.1 18.8 - - + +
67H PHE* 5.0 0.9 - - - -
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Residues in contact with ALA 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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37H LEU* 4.7 3.9 - - + +
38H ALA* 1.3 75.3 - - - +
40H GLU* 1.3 63.2 + - - +
41H GLY 4.4 5.2 - - - +
44H ASN 5.4 0.2 - - - +
45H ARG 5.2 2.7 - - - +
46H LEU 4.8 2.9 - - - +
47H CYS* 3.7 21.5 - - + +
48H PHE* 5.7 0.7 - - - -
64H ILE* 4.1 12.6 + - - +
67H PHE* 5.1 6.9 - - + -
111H HIS* 3.1 30.2 + - + +
137H LEU* 4.9 16.8 - - + +
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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
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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