Contacts of the strand formed by residues 51 - 60 (chain H) 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 LEU 51 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU* 4.7 7.0 - - + -
29H VAL* 4.5 14.4 - - + -
42H LEU* 3.7 17.7 - - + -
44H SER 3.5 11.4 - - - +
45H THR* 4.2 4.0 - - - +
49H PHE* 3.7 16.6 - - + +
50H ASN* 1.3 79.9 - - - +
52H GLN* 1.3 60.1 + - - +
53H LEU* 3.8 5.1 + - + +
72H PHE* 3.5 3.1 - - - -
73H ILE* 3.0 63.3 + - + +
78H VAL* 5.2 3.1 - - + -
81H ILE* 3.5 31.9 - - + -
18N PHE* 4.9 7.1 - - - -
49N PHE* 5.7 0.6 - - - -
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Residues in contact with GLN 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LEU* 3.7 3.7 - - - +
43H VAL* 2.8 60.1 + - + +
44H SER* 2.9 31.2 + - - +
51H LEU* 1.3 70.1 - - - +
53H LEU* 1.3 61.9 + - - +
70H GLU* 2.9 29.3 + - - +
71H ILE 3.4 6.7 - - - +
72H PHE* 3.5 38.7 - - + +
18N PHE* 4.6 2.2 - - + -
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Residues in contact with LEU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H VAL* 3.8 28.3 - - + -
29H VAL* 4.5 11.4 - - + -
38H TYR* 4.1 19.5 - - + +
39H ARG* 3.5 31.4 - - - +
40H GLY* 3.8 7.6 - - - -
41H THR 3.5 10.1 - - - +
42H LEU* 4.2 7.0 - - + -
43H VAL* 4.5 0.9 - - - -
51H LEU* 3.8 7.2 + - + +
52H GLN* 1.3 76.9 - - - +
54H ASN* 1.3 62.5 + - - +
56H ALA* 3.9 13.5 - - + -
69H GLY 4.2 1.1 - - - +
70H GLU* 3.6 5.2 - - - +
71H ILE* 2.8 40.6 + - + +
73H ILE* 5.0 8.5 - - + -
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Residues in contact with ASN 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H GLY* 3.1 1.6 - - - -
41H THR* 2.5 49.9 + - + +
43H VAL* 3.4 20.8 - - + +
53H LEU* 1.3 73.3 - - - +
55H GLU* 1.3 103.8 + - - +
56H ALA 3.3 2.5 - - - -
69H GLY 4.5 0.8 - - - -
70H GLU* 2.6 30.0 + - - +
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Residues in contact with GLU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ARG* 5.0 9.6 + - - +
39H ARG 3.4 5.9 - - - +
40H GLY* 3.7 4.3 - - - -
41H THR* 5.1 4.7 - - - +
54H ASN* 1.3 93.9 + - - +
56H ALA* 1.3 65.4 + - - +
57H GLU* 3.6 4.0 + - - +
67H THR* 4.8 7.0 - - + +
68H LEU 4.1 0.7 - - - -
69H GLY* 3.5 11.1 + - - -
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Residues in contact with ALA 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H TYR* 5.4 1.1 - - + -
39H ARG 2.9 10.1 - - - +
53H LEU* 3.9 14.1 - - + -
54H ASN 3.3 0.8 - - - -
55H GLU* 1.3 75.6 - - - +
57H GLU* 1.3 58.8 + - - +
67H THR* 2.9 16.3 - - - +
68H LEU* 2.7 36.1 + - + +
69H GLY 3.5 3.8 - - - +
71H ILE* 3.2 33.4 - - + -
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ARG* 4.5 12.3 + - - +
38H TYR* 3.7 3.0 - - - -
39H ARG* 2.6 35.8 + - + +
55H GLU 4.5 3.4 - - - +
56H ALA* 1.3 75.0 - - - +
58H GLU* 1.3 63.1 + - - +
59H PHE* 3.2 33.0 + - + -
64H SER* 3.4 22.3 + - - +
66H GLY 3.2 18.8 - - - +
67H THR* 3.8 12.3 + - + +
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Residues in contact with GLU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H THR* 4.1 14.3 - - + +
38H TYR* 3.3 41.3 + - + -
56H ALA 4.2 0.2 - - - -
57H GLU* 1.3 73.4 - - - +
59H PHE* 1.3 67.3 + - - +
60H VAL* 5.0 4.3 - - + -
64H SER* 3.4 1.9 - - - -
65H HIS* 2.9 51.4 + - + +
66H GLY 2.9 12.2 + - - +
68H LEU* 4.0 17.5 - - + +
30N LYS* 6.0 1.4 - - - -
80N TYR* 4.6 6.2 + - - -
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Residues in contact with PHE 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ARG* 6.3 0.2 - - - -
35H SER 3.5 1.9 - - - +
36H THR* 3.3 3.7 - - - -
37H GLU* 2.8 47.0 + - + +
39H ARG* 3.4 58.3 - - + +
57H GLU* 3.2 56.5 - - + -
58H GLU* 1.3 75.0 - - - +
60H VAL* 1.3 62.1 + - - +
61H ALA 4.0 0.4 + - - -
62H GLY* 4.0 14.2 + - - -
63H VAL 3.3 6.7 - - - +
64H SER* 3.6 24.9 - - - -
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Residues in contact with VAL 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 4.7 7.0 - - + -
65D HIS* 3.2 24.2 - - + -
35H SER* 3.6 11.7 - - - +
36H THR* 4.8 10.3 - - + +
58H GLU* 5.0 8.3 - - + -
59H PHE* 1.3 73.1 - - - +
61H ALA* 1.3 73.0 + - + +
62H GLY 2.9 3.4 - - - -
63H VAL 2.8 16.9 + - - -
65H HIS* 3.5 41.1 - - + +
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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