Contacts of the helix formed by residues 26 - 33 (chain K) in PDB entry 6GYS
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 SER 26 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K ILE 4.1 1.9 + - - -
23K ALA* 2.9 12.0 + - - +
24K GLU 4.0 0.7 - - - -
25K ARG* 1.3 73.7 - - - +
27K LEU* 1.3 52.6 + - - +
28K LEU* 4.2 0.3 - - - +
29K LEU* 2.9 28.5 + - - +
30K LYS 2.6 31.5 + - - -
141K LEU* 2.6 38.3 + - - +
143K ILE* 3.7 16.9 - - - +
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Residues in contact with LEU 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402H PHE* 5.4 8.7 - - + -
378I ASP* 4.2 14.1 - - + +
382I TYR* 3.5 10.6 + - + +
24K GLU 3.4 20.0 - - - +
25K ARG 3.1 8.6 + - - +
26K SER* 1.3 69.0 - - - +
28K LEU* 1.3 58.9 - - - +
30K LYS* 3.6 18.4 - - + -
31K ASN* 2.8 38.4 + - - +
105K GLU* 5.2 11.0 - - - +
141K LEU 3.4 0.2 + - - -
142K ASN* 3.1 39.9 + - - +
144K LYS* 5.7 3.8 - - + +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430I LYS* 3.6 25.4 - - + +
433I HIS* 3.7 30.8 - - + +
434I TYR* 3.8 27.2 + - + +
26K SER 3.2 0.2 - - - -
27K LEU* 1.3 77.0 - - - +
29K LEU* 1.3 59.8 + - - +
31K ASN* 3.2 6.7 + - - +
32K TYR* 2.9 25.6 + - + +
77K MET* 3.7 24.7 - - + -
140K TYR* 3.3 23.8 - - + +
141K LEU* 3.5 26.4 + - + +
142K ASN* 3.9 6.9 - - + +
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Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 3.9 19.5 - - + -
8K LEU* 3.8 28.0 - - + -
18K VAL* 5.5 0.9 - - + -
23K ALA* 3.7 31.9 - - + +
26K SER* 2.9 23.0 + - - +
28K LEU* 1.3 81.7 - - + +
30K LYS* 1.3 60.5 + - - +
32K TYR* 3.1 29.2 + - + +
33K LEU* 2.9 30.8 + - + +
75K ILE* 5.6 0.4 - - + +
77K MET* 3.8 21.3 - - + -
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Residues in contact with LYS 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398H LYS* 5.3 8.9 - - - +
402H PHE* 4.4 14.6 - - - -
382I TYR* 3.1 38.6 + - + +
20K LYS* 5.7 1.8 - - - +
23K ALA 3.5 4.4 + - - +
24K GLU* 3.3 54.1 + - + +
26K SER 2.6 19.4 + - - +
27K LEU* 3.8 13.9 - - + +
28K LEU 3.3 0.2 - - - -
29K LEU* 1.3 72.5 - - - +
31K ASN* 1.3 59.9 + - - +
33K LEU* 3.3 30.7 - - + +
34K ASN* 3.5 7.6 + - - +
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Residues in contact with ASN 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377I LEU* 6.1 1.2 - - - +
378I ASP* 3.3 20.8 + - - -
381I GLN* 2.9 36.3 - - - +
382I TYR* 2.7 27.4 + - - -
404I LEU* 5.3 1.2 - - - +
434I TYR* 4.3 16.8 + - + +
437I VAL* 5.9 1.0 - - - +
27K LEU* 2.8 26.3 + - - +
28K LEU* 3.5 8.6 - - - +
30K LYS* 1.3 74.7 - - - +
32K TYR* 1.3 58.5 + - - +
33K LEU 3.1 0.4 - - - -
34K ASN* 3.0 29.8 + - - +
35K ASP* 3.6 2.8 + - - +
142K ASN* 5.6 0.8 - - - +
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Residues in contact with TYR 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433I HIS* 4.3 12.1 - + + +
437I VAL* 3.6 30.1 - - + -
28K LEU* 2.9 13.7 + - + +
29K LEU* 3.1 30.0 + - + +
31K ASN* 1.3 73.6 - - - +
33K LEU* 1.3 60.9 + - - +
34K ASN 3.1 0.2 - - - -
35K ASP* 2.9 58.1 + - + +
75K ILE* 3.8 23.1 - - + +
76K VAL* 2.8 32.4 + - - +
77K MET* 4.2 10.5 - - + -
78K PRO* 6.2 0.7 - - + -
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Residues in contact with LEU 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 3.7 29.6 - - + -
20K LYS* 3.1 53.3 - - + +
23K ALA* 4.5 10.3 - - + -
24K GLU* 4.7 3.8 - - + -
29K LEU* 2.9 17.5 + - + +
30K LYS* 3.3 31.6 - - + +
31K ASN 3.1 0.2 - - - -
32K TYR* 1.3 78.2 - - - +
34K ASN* 1.3 62.1 + - - +
35K ASP 3.6 3.8 + - - +
75K ILE* 5.2 9.4 - - + -
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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