Contacts of the strand formed by residues 26 - 34 (chain K) in PDB entry 1YHQ
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 ALA 26 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K CYS* 3.1 27.2 - - - +
22K ASP* 4.3 4.3 - - - +
24K THR* 3.5 13.9 + - - +
25K GLY* 1.3 80.0 + - - +
27K ARG* 1.3 60.1 + - - +
29K LEU* 4.2 3.4 - - + -
57K VAL* 3.6 35.7 - - + -
59K LYS 3.7 4.0 - - - -
64K MET* 4.0 6.0 - - + +
97K ILE* 3.9 11.4 - - + -
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Residues in contact with ARG 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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19K THR* 3.8 7.8 - - - +
20K CYS* 3.0 25.4 + - - +
25K GLY 4.6 3.6 + - - +
26K ALA* 1.3 75.9 - - - +
28K GLU* 1.3 57.6 + - + +
59K LYS* 2.6 23.5 + - + +
60K GLY* 4.1 14.9 - - - +
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Residues in contact with GLU 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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17K LEU* 3.6 33.6 - - + +
18K ILE 3.5 9.1 - - - +
27K ARG* 1.3 79.1 - - + +
29K LEU* 1.3 70.5 + - - +
57K VAL* 3.7 5.2 - - - +
58K THR* 2.8 55.3 + - - +
59K LYS* 3.1 45.1 + - + +
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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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17K LEU* 3.4 2.6 - - - -
18K ILE* 2.8 51.7 + - + +
19K THR 4.5 0.4 - - - +
20K CYS* 3.6 35.9 - - + -
26K ALA* 4.2 10.8 - - + -
28K GLU* 1.3 81.4 - - - +
30K LYS* 1.3 58.8 + - - +
55K VAL* 3.3 23.3 - - + -
56K SER 3.6 1.3 - - - -
57K VAL* 3.6 29.8 - - + -
58K THR* 4.6 0.2 - - - -
69K LEU* 6.1 0.4 - - + -
71K ALA* 4.6 6.5 - - + -
95K ALA* 4.2 22.0 - - + +
97K ILE* 4.3 14.6 - - + -
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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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19920 U 3.3 14.8 + - - -
19930 C 2.7 46.9 + - + +
19940 A 5.7 0.6 - - - +
15K GLY* 3.9 21.1 - - - +
16K SER 3.3 3.6 - - - -
17K LEU* 3.7 11.0 - - + -
29K LEU* 1.3 72.1 - - - +
31K VAL* 1.3 74.2 + - - +
32K ILE* 3.5 2.3 + - + +
55K VAL* 3.0 17.7 - - - +
56K SER* 2.9 31.6 + - - +
58K THR* 3.6 18.7 + - - +
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Residues in contact with VAL 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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19930 C 5.2 1.0 + - - -
12K LEU* 4.7 9.6 - - + -
13K GLU 3.4 24.9 - - - +
14K LYS* 4.2 5.5 - - - +
15K GLY* 2.7 29.3 + - - -
16K SER* 2.9 22.2 + - - +
18K ILE* 4.2 15.9 - - + -
30K LYS* 1.3 75.0 - - - +
32K ILE* 1.3 61.7 + - - +
33K SER 4.2 15.3 - - - +
34K VAL* 5.0 1.8 - - + -
47K ALA* 4.7 8.7 - - + -
53K ILE* 4.0 31.2 - - + -
54K THR 4.0 2.9 - - - -
55K VAL* 4.2 2.2 - - - -
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Residues in contact with ILE 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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19930 C 3.3 66.0 - - + +
25960 A 3.4 23.8 - - - +
14K LYS* 2.6 41.7 + - - +
30K LYS* 3.7 10.3 - - + +
31K VAL* 1.3 80.4 - - - +
33K SER* 1.3 60.7 + - - +
54K THR* 3.0 11.5 + - + +
55K VAL* 4.0 4.7 - - - +
56K SER* 3.5 25.6 - - - +
68K VAL* 4.6 10.3 - - + -
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Residues in contact with SER 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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25960 A 2.5 32.5 + - - +
25970 U 3.1 29.3 + - - -
88120 CL 3.3 14.5 - - - +
14K LYS* 5.4 1.3 - - - -
31K VAL* 4.2 3.1 - - - +
32K ILE* 1.3 82.9 + - - +
34K VAL* 1.3 66.8 + - - +
45K PRO* 6.0 0.4 - - - -
53K ILE* 3.2 9.9 - - - +
54K THR* 2.8 29.6 + - - -
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Residues in contact with VAL 34 (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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25970 U 2.9 18.7 + - - -
13K GLU 6.3 0.2 - - - -
14K LYS* 6.1 0.9 - - + +
31K VAL* 5.0 4.0 - - + -
33K SER* 1.3 79.0 - - - +
35K HIS* 1.3 72.8 + - - +
37K TYR* 3.1 31.8 + - + +
45K PRO* 4.8 8.6 - - + +
46K LYS* 3.3 32.5 - - - +
47K ALA* 3.3 18.6 - - + -
51K ASP* 4.2 28.9 - - + +
52K LYS 4.0 2.2 - - - +
53K ILE* 4.3 0.9 - - + -
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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