Contacts of the strand formed by residues 31 - 37 (chain K) in PDB entry 2AK4
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 THR 31 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27K TYR* 3.3 4.1 - - - -
28K VAL* 2.9 36.0 + - - +
29K ASP 3.3 0.4 - - - -
30K ASP* 1.3 76.0 - - - +
32K GLN* 1.3 74.3 + - - +
33K PHE* 3.6 2.6 + - - +
49K ALA* 4.5 1.1 - - + -
51K TRP* 4.4 7.9 - - + -
179K LEU* 4.0 16.4 - - + +
209K TYR* 2.6 32.7 + - - -
239K ARG* 4.4 13.9 - - - +
1001K IOD 4.2 25.4 - - + -
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Residues in contact with GLN 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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25K VAL* 3.7 18.5 - - + +
26K GLY 3.4 15.9 - - - +
27K TYR* 3.5 35.4 + - + +
30K ASP 4.0 0.6 + - - -
31K THR* 1.3 81.7 - - - +
33K PHE* 1.3 59.8 + - - +
34K VAL 3.2 19.6 + - - +
35K ARG* 3.7 0.4 - - - +
48K ARG* 3.5 34.5 + - + +
49K ALA* 3.7 1.6 - - - +
239K ARG* 4.7 3.0 + - - +
52L SER* 5.6 2.3 - - - -
53L ASP* 3.0 36.7 + - - +
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Residues in contact with PHE 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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5K MET* 4.4 3.8 - - + -
7K TYR* 3.2 32.1 - + - -
26K GLY* 3.0 30.1 + - - -
27K TYR 3.5 12.6 - - - -
28K VAL* 3.7 24.2 - - + -
31K THR 4.1 0.2 - - - -
32K GLN* 1.3 73.7 - - - +
34K VAL* 1.3 71.9 + - + +
47K PRO* 3.6 1.2 - - - +
48K ARG* 2.7 26.5 + - - -
49K ALA* 3.9 9.4 - - + +
51K TRP* 3.4 27.6 - + + -
52K ILE* 3.4 30.9 - - + +
59K TYR* 4.0 9.9 - - - -
171K TYR* 3.9 23.8 - + - -
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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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7K TYR* 3.8 15.0 - - + +
25K VAL* 3.4 1.2 - - - -
26K GLY* 3.0 43.8 + - - +
32K GLN* 3.2 12.1 + - - -
33K PHE* 1.3 101.2 - - + +
35K ARG* 1.3 64.4 + - - +
45K THR* 3.3 31.0 - - + -
46K GLU 3.4 10.3 - - - +
48K ARG* 3.7 5.2 - - - +
59K TYR* 5.4 2.2 - - - +
60K TRP* 3.9 12.3 - - + -
63K ASN* 4.4 6.7 - - - +
67K PHE* 5.2 3.6 - - + -
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Residues in contact with ARG 35 (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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23K ILE* 6.2 0.7 - - + -
24K ALA 3.3 10.1 - - - +
25K VAL* 4.2 2.5 - - + -
32K GLN* 3.7 2.7 - - - +
34K VAL* 1.3 76.5 - - - +
36K PHE* 1.3 65.4 + - - +
37K ASP* 5.4 7.1 - - - +
44K ARG 3.9 0.5 - - - +
45K THR* 3.4 6.9 - - - +
46K GLU* 2.6 68.8 + - + +
48K ARG* 3.1 43.7 - - - +
67K PHE* 5.5 0.9 - - - -
51L HIS 5.8 0.6 + - - -
53L ASP* 2.7 51.1 + - + +
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Residues in contact with PHE 36 (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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22K PHE* 3.9 13.9 - + - -
23K ILE* 3.3 7.7 - - - +
24K ALA* 2.8 35.1 + - + +
35K ARG* 1.3 78.7 - - - +
37K ASP* 1.3 62.8 + - - +
38K SER* 3.9 13.7 - - - -
43K PRO* 3.7 32.8 - - + -
44K ARG 3.8 18.6 - - - -
45K THR* 3.7 17.0 - - - +
64K THR* 4.3 12.3 - - + -
67K PHE* 3.5 50.0 - - + -
68K LYS* 4.2 9.6 - - + -
71K THR* 3.6 20.4 - - - -
1009K IOD 4.4 1.3 - - + -
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Residues in contact with ASP 37 (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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21K ARG* 3.0 36.4 + - - +
22K PHE 3.7 2.9 - - - -
23K ILE* 4.1 10.1 - - + +
35K ARG* 5.4 9.1 - - - +
36K PHE* 1.3 80.7 - - - +
38K SER* 1.3 62.1 + - - +
39K ASP* 2.8 32.2 + - - +
40K ALA* 3.6 15.7 + - + +
43K PRO* 3.4 15.4 - - - +
44K ARG 4.7 3.5 + - - -
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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