Contacts of the strand formed by residues 34 - 40 (chain D) in PDB entry 6QCG
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 GLY 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASP 3.6 4.2 - - - +
30D ILE 3.7 0.2 - - - -
31D SER* 3.1 32.2 + - - -
32D SER 3.1 0.6 - - - -
33D SER* 1.3 81.0 - - - +
35D VAL* 1.3 57.3 + - - -
36D ASN* 5.1 3.9 + - - -
52D LEU 3.6 8.3 - - - -
54D SER* 3.6 5.6 - - - -
60D TYR* 3.2 26.3 + - - -
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D PHE* 4.8 6.3 - - + -
28D TRP* 3.3 39.3 - - + -
29D ASP 3.6 3.1 - - - +
30D ILE* 3.8 20.6 - - + -
34D GLY* 1.3 75.2 - - - -
36D ASN* 1.3 67.3 + - - +
37D LEU 4.3 0.2 - - - -
50D LEU* 4.0 1.8 - - + +
51D THR* 3.5 4.0 + - - -
52D LEU* 2.8 53.8 + - + +
57D PHE* 4.5 13.0 - - + -
60D TYR* 3.8 20.4 - - + +
90D LEU* 6.1 3.8 - - + -
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D CYS 4.1 0.2 - - - +
29D ASP* 2.7 56.6 + - + +
31D SER* 5.9 0.6 + - - -
33D SER* 6.1 2.0 - - - -
34D GLY 5.1 3.0 + - - -
35D VAL* 1.3 79.1 + - - +
37D LEU* 1.3 58.0 + - - +
38D GLN 4.3 0.2 - - - -
49D GLN* 3.3 24.5 + - - +
50D LEU 3.5 6.5 - - - +
51D THR* 3.6 21.2 + - - +
125D GLN* 6.2 0.9 - - - +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.2 19.3 - - + -
23D ILE* 4.6 9.6 - - + -
26D ALA* 4.0 23.1 - - + -
27D CYS 4.0 14.1 - - - +
28D TRP* 3.5 46.4 - - + +
35D VAL* 4.3 0.8 - - - +
36D ASN* 1.3 73.3 - - - +
38D GLN* 1.3 74.6 + - - +
39D SER* 4.1 6.5 - - - +
48D VAL* 5.0 5.2 - - + +
49D GLN* 3.4 4.7 + - - -
50D LEU* 2.8 50.7 + - + +
72D LEU* 4.8 2.0 - - + -
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D CYS* 4.4 10.2 + - - +
29D ASP* 5.4 2.4 + - - -
36D ASN 4.3 0.4 + - - -
37D LEU* 1.3 77.0 - - - +
39D SER* 1.3 64.5 + - - +
47D LEU* 4.2 12.5 - - + +
48D VAL 3.2 12.8 - - - +
49D GLN* 3.6 14.0 - - - +
123D VAL* 5.8 2.3 - - - +
125D GLN* 2.6 44.9 + - + +
126D LEU* 2.6 45.6 + - - +
128D ILE* 3.2 29.9 - - - +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE* 4.0 26.8 - - - +
25D GLU 4.1 8.8 + - - -
26D ALA* 4.4 10.5 - - - -
27D CYS 5.9 0.2 - - - -
37D LEU* 4.1 8.0 - - - +
38D GLN* 1.3 74.8 - - - +
40D MET* 1.3 71.9 + - - +
47D LEU* 3.4 4.5 - - - +
48D VAL* 2.7 40.7 + - - +
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE* 3.9 4.9 - - - +
39D SER* 1.3 87.4 + - - +
41D ASP* 1.3 69.2 + - - +
44D HIS* 3.4 54.7 - - + +
46D SER 3.4 16.4 - - - +
47D LEU* 3.9 19.3 - - + -
126D LEU* 4.1 25.6 - - + -
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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