Contacts of the strand formed by residues 36 - 44 (chain K) in PDB entry 1N9S
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 36 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LYS* 3.8 7.3 - - - +
31K LEU* 3.3 40.3 + - + +
33K PHE* 4.6 1.4 + - - -
34K ASN* 3.5 22.7 + - - +
35K SER* 1.3 76.6 - - - +
37K GLU* 1.3 65.0 - - - +
38K TYR* 3.9 35.0 - - + +
58K GLU* 4.2 11.9 - - + +
59K PHE 3.3 8.1 - - - +
60K VAL* 4.4 10.3 - - + +
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Residues in contact with GLU 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K GLY* 3.9 12.1 - - - -
29K VAL 3.3 22.9 - - - +
30K LYS* 4.6 18.4 - - + +
35K SER 5.4 0.4 - - - +
36K THR* 1.3 76.2 - - - +
38K TYR* 1.3 65.3 + - - +
39K ARG* 2.5 44.4 + - + +
57K GLU 3.0 4.2 - - - +
58K GLU 3.3 0.2 - - - -
59K PHE* 2.6 47.6 + - + +
80K TYR* 4.8 2.4 + - - -
82K ARG* 3.1 29.8 + - - +
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Residues in contact with TYR 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J LEU* 4.2 6.5 - - + +
80J TYR* 3.4 28.6 - + - -
28K GLY* 3.8 0.2 - - - -
29K VAL* 2.7 36.9 + - - +
31K LEU* 3.2 40.5 - - + +
36K THR* 3.9 9.1 - - + +
37K GLU* 1.3 72.2 - - - +
39K ARG* 1.3 61.6 + - - +
53K LEU* 3.9 15.9 - - + -
56K ALA* 5.0 0.9 - - + -
57K GLU 3.2 2.7 - - - -
58K GLU* 3.1 50.3 + - + -
68K LEU* 3.8 20.0 - - + -
71K ILE* 4.0 9.0 - - + -
73K ILE* 3.8 21.5 - - + -
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Residues in contact with ARG 39 (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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26K ARG* 4.6 11.8 + - - +
27K VAL 3.2 7.2 - - - +
28K GLY* 4.2 1.3 - - - -
37K GLU* 2.5 33.4 + - + +
38K TYR* 1.3 77.2 - - - +
40K GLY* 1.3 59.4 + - - +
53K LEU* 3.8 2.0 - - - -
55K GLU 3.9 2.1 - - - +
56K ALA* 3.0 3.8 - - - -
57K GLU* 2.6 42.1 + - + +
59K PHE* 3.3 54.4 - - + +
62K GLY* 4.4 15.0 + - - -
82K ARG* 3.8 13.3 - - - +
84K LEU* 3.9 24.2 - - + -
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Residues in contact with GLY 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ARG* 3.4 18.8 - - - +
27K VAL* 2.9 33.7 + - - +
39K ARG* 1.3 75.8 - - - +
41K THR* 1.3 64.3 + - - -
42K LEU 3.9 0.2 - - - -
53K LEU* 3.5 16.2 - - - +
54K ASN 3.5 11.2 - - - -
55K GLU 4.3 1.3 - - - -
56K ALA* 4.2 0.7 - - - -
84K LEU* 4.8 0.2 - - - +
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Residues in contact with THR 41 (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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24K ASN* 4.1 27.8 - - - +
25K HIS 3.3 12.1 + - - +
26K ARG* 4.2 9.9 + - - +
40K GLY* 1.3 74.4 - - - -
42K LEU* 1.3 63.2 + - - +
43K VAL* 3.1 9.3 + - + -
53K LEU* 3.5 2.3 - - - -
54K ASN* 2.7 44.0 + - + +
55K GLU* 3.4 27.2 + - - +
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Residues in contact with LEU 42 (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 LEU* 4.4 10.8 - - + +
22K LEU* 3.7 43.1 - - + +
23K VAL* 3.4 6.9 - - + +
24K ASN* 2.9 23.8 + - - -
25K HIS 3.0 10.5 + - - +
27K VAL* 4.1 17.3 - - + -
40K GLY 3.9 1.8 + - - -
41K THR* 1.3 68.6 - - - +
43K VAL* 1.3 62.6 + - - +
44K SER 2.8 29.4 - - - +
45K THR* 3.6 13.5 - - - +
51K LEU* 4.2 13.9 - - + -
52K GLN 3.6 9.4 - - - +
53K LEU* 4.1 8.5 - - + +
81K ILE* 5.6 4.5 - - + -
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Residues in contact with VAL 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K VAL* 4.3 10.4 - - - +
24K ASN* 5.6 3.0 + - - +
41K THR* 3.9 5.2 - - + +
42K LEU* 1.3 74.4 - - - +
44K SER* 1.3 64.8 + - - +
52K GLN* 2.9 44.0 + - - +
54K ASN* 3.6 33.7 - - + +
70K GLU* 3.8 9.4 - - - +
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Residues in contact with SER 44 (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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18J PHE* 3.9 12.0 + - - -
23K VAL* 4.7 9.9 - - - -
42K LEU* 2.8 16.9 - - - +
43K VAL* 1.3 85.9 - - - +
45K THR* 1.3 76.8 + - - +
51K LEU* 3.9 0.5 - - - +
52K GLN* 3.4 33.8 + - - +
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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