Contacts of the strand formed by residues 32 - 39 (chain N) in PDB entry 6C23
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 TYR 32 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A PRO* 4.5 3.8 - - + -
536A THR* 4.6 6.2 + - - +
24N TRP* 3.3 33.7 + + - -
28N THR* 3.2 33.6 + - + +
29N PRO 4.2 10.3 - - - +
30N PHE 5.4 0.2 - - - -
31N LEU* 1.3 91.1 - - + +
33N ASP* 1.3 73.8 + - - +
34N LEU 3.9 9.9 - - - +
35N VAL* 3.7 19.5 - - + -
368N PHE* 3.6 23.9 - + - -
369N ILE 4.5 0.3 + - - -
370N HIS* 2.4 37.0 + + - -
402N TRP* 3.8 24.9 - + - -
403N GLN 3.6 12.3 - - - +
404N MET* 4.2 1.3 - - - -
405N ALA* 3.6 10.4 - - - +
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Residues in contact with ASP 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A PRO* 4.0 7.6 - - - +
534A LYS 3.0 19.8 - - - +
535A ARG* 3.4 43.8 + - + +
536A THR* 4.4 11.8 + - - +
32N TYR* 1.3 85.9 - - - +
34N LEU* 1.3 59.8 + - - +
403N GLN* 2.9 17.5 + - + +
404N MET 3.3 6.2 - - - +
405N ALA* 3.9 0.9 - - - +
406N GLU* 3.0 41.4 + - - +
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Residues in contact with LEU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A CYS* 4.9 0.2 - - - -
533A PRO* 3.6 21.8 - - - +
534A LYS* 3.8 14.4 - - - +
535A ARG* 5.0 6.7 - - - +
32N TYR* 4.0 0.6 - - - +
33N ASP* 1.3 80.9 - - - +
35N VAL* 1.3 77.8 + - - +
36N MET* 4.0 22.9 - - + -
86N LEU* 3.9 32.8 - - + -
87N PRO* 4.9 7.9 - - + +
389N VAL* 5.1 4.5 - - + -
401N VAL* 4.4 9.9 - - + +
402N TRP* 3.0 9.4 - - - +
403N GLN* 3.0 46.3 + - + +
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Residues in contact with VAL 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A CYS* 3.8 0.2 - - - -
532A ARG* 3.3 25.4 + - + +
533A PRO* 3.3 38.0 - - + +
24N TRP* 4.8 15.3 - - + -
28N THR* 4.9 1.1 - - + -
32N TYR* 3.7 34.8 - - + -
34N LEU* 1.3 81.2 - - - +
36N MET* 1.3 72.9 + - - +
37N THR* 4.5 11.9 - - - +
370N HIS* 5.9 0.2 - - + -
400N GLN* 5.7 3.4 - - + -
401N VAL 3.4 6.1 - - - -
402N TRP* 3.9 12.6 - - + -
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Residues in contact with MET 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 5.9 3.6 - - + -
530A VAL 3.8 6.7 - - - +
531A CYS* 4.0 22.9 - - + -
34N LEU* 4.0 15.3 - - + -
35N VAL* 1.3 81.2 - - - +
37N THR* 1.3 64.3 + - - +
38N HIS* 4.0 1.3 - - + +
84N VAL* 5.9 1.1 - - - -
85N GLN 3.2 27.1 - - - +
86N LEU* 3.7 23.6 - - + -
87N PRO* 4.6 5.2 - - + -
113N GLY* 4.9 2.5 - - - -
114N LYS* 4.7 9.2 - - - +
115N ILE* 4.2 21.5 - - + -
399N MET 3.5 2.3 - - - +
400N GLN* 3.3 4.5 - - - -
401N VAL* 2.8 47.8 + - + +
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Residues in contact with THR 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 3.7 3.2 - - - +
530A VAL* 2.6 55.7 + - + +
531A CYS* 4.7 0.2 - - - +
532A ARG* 5.8 0.3 - - - +
21N TYR* 5.0 9.8 + - - +
24N TRP* 5.6 1.4 - - - -
35N VAL* 4.2 10.5 - - - +
36N MET* 1.3 76.0 - - - +
38N HIS* 1.3 70.1 + - - +
398N ILE* 3.8 29.6 - - + -
399N MET 3.7 2.0 - - - -
400N GLN* 3.4 22.1 + - + +
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Residues in contact with HIS 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A HIS* 3.4 22.7 + + + -
528A ILE 3.3 23.8 + - - -
529A LEU* 4.0 12.7 - - + +
36N MET* 4.0 0.6 - - + -
37N THR* 1.3 86.4 - - - +
39N ALA* 1.3 88.2 + - - +
40N LEU* 3.7 18.3 - - + +
115N ILE* 3.6 43.5 - - + +
116N GLU* 5.5 4.0 - - - -
117N ILE* 4.6 8.9 - - + +
398N ILE* 3.8 2.9 - - - +
399N MET* 3.1 36.1 + - + +
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Residues in contact with ALA 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ILE* 4.4 21.1 - - + -
526A THR 4.3 5.6 - - - +
527A HIS* 3.1 19.2 + - - -
528A ILE* 3.4 29.6 + - + +
561M HIS* 5.1 4.7 - - + -
38N HIS* 1.3 91.7 + - - +
40N LEU* 1.3 62.5 + - - +
397N ASN 3.7 4.7 - - - +
398N ILE* 4.5 8.5 - - + -
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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