Contacts of the strand formed by residues 51 - 60 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E PHE* 5.7 0.2 - - - -
29F VAL* 4.2 17.5 - - + -
42F LEU* 3.5 22.9 - - + -
44F SER 3.6 4.0 - - - +
45F THR* 4.1 7.6 - - + -
49F PHE* 3.5 16.8 - - + +
50F ASN* 1.3 75.3 - - - +
52F GLN* 1.3 57.6 + - - +
53F LEU* 4.2 5.8 + - + -
71F ILE 4.0 0.2 - - - +
72F PHE* 3.3 4.3 - - - +
73F ILE* 2.6 76.5 + - + +
78F VAL* 5.0 3.6 - - + -
81F ILE* 3.4 33.4 - - + -
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Residues in contact with GLN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.4 7.4 - - - +
43F VAL* 3.0 51.5 + - - +
44F SER* 3.3 24.6 + - - +
51F LEU* 1.3 74.7 - - - +
53F LEU* 1.3 63.7 + - - +
70F GLU* 2.2 35.7 + - - +
71F ILE 3.2 7.6 - - - +
72F PHE* 3.3 42.8 - - + -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 4.1 24.0 - - + -
29F VAL* 4.3 12.3 - - + -
38F TYR* 3.9 32.3 - - + +
39F ARG 3.9 20.4 - - - +
40F GLY* 4.0 9.4 - - - +
41F THR 3.8 0.7 - - - +
42F LEU* 4.2 13.2 - - + -
43F VAL* 5.0 0.7 - - - -
51F LEU* 4.1 4.9 + - + -
52F GLN* 1.3 80.5 - - - +
54F ASN* 1.3 62.7 + - - +
56F ALA* 4.1 4.9 - - + -
70F GLU* 3.3 13.4 - - - +
71F ILE* 2.8 51.0 + - + +
73F ILE* 4.3 5.2 - - + -
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Residues in contact with ASN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLY* 3.5 1.4 - - - -
41F THR* 2.9 44.1 + - + +
43F VAL* 3.8 18.1 - - + +
53F LEU* 1.3 73.5 - - - +
55F GLU* 1.3 98.1 + - + +
56F ALA 3.2 1.5 + - - -
70F GLU* 2.2 31.8 + - - +
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ARG* 4.9 13.4 + - - +
39F ARG 3.4 6.6 - - - +
40F GLY* 4.1 2.4 - - - -
41F THR* 5.4 2.7 - - - +
54F ASN* 1.3 91.6 + - - +
56F ALA* 1.3 66.9 + - - +
57F GLU* 3.5 3.6 + - - +
67F THR* 4.8 5.7 - - + +
68F LEU 4.2 2.2 - - - -
69F GLY 3.7 10.3 + - - -
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Residues in contact with ALA 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F TYR* 5.2 1.1 - - + -
39F ARG 3.1 9.4 - - - +
53F LEU* 4.1 9.2 - - + -
54F ASN 3.2 2.4 - - - -
55F GLU* 1.3 77.0 - - - +
57F GLU* 1.3 59.5 + - - +
67F THR* 3.1 9.5 - - - +
68F LEU* 3.1 37.0 + - + +
69F GLY 3.3 10.8 + - - +
71F ILE* 3.6 37.5 - - + -
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ARG* 4.8 11.6 + - - +
38F TYR* 3.5 2.6 - - - -
39F ARG* 2.8 33.6 + - + +
55F GLU 4.5 3.1 - - - +
56F ALA* 1.3 76.9 - - - +
58F GLU* 1.3 61.9 + - - +
59F PHE* 3.1 34.8 - - + -
64F SER* 2.6 30.5 + - - +
66F GLY 3.2 22.2 - - - +
67F THR* 4.2 9.5 + - + +
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS* 5.9 2.9 - - - -
80E TYR* 4.7 6.6 + - - -
36F THR* 4.1 12.8 - - + +
37F GLU 3.7 2.9 - - - -
38F TYR* 3.6 37.7 + - + -
56F ALA 4.2 0.8 - - - -
57F GLU* 1.3 72.8 - - - +
59F PHE* 1.3 63.5 + - - +
60F VAL* 4.2 6.7 - - + -
64F SER* 3.4 6.2 + - - -
65F HIS* 2.8 55.2 + - + +
66F GLY 3.1 13.8 + - - +
68F LEU* 4.3 14.5 - - + +
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Residues in contact with PHE 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ARG* 6.1 0.9 - - - -
35F SER 3.4 1.6 - - - +
36F THR* 3.3 4.8 - - - -
37F GLU* 2.5 46.0 + - + +
39F ARG* 3.1 62.6 - - + +
57F GLU* 3.1 62.4 - - + -
58F GLU* 1.3 74.9 - - - +
60F VAL* 1.3 63.3 + - - +
61F ALA 3.8 0.7 + - - -
62F GLY* 3.9 14.8 + - - -
63F VAL 3.8 4.7 - - - +
64F SER* 3.7 24.0 - - - -
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Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F SER* 3.4 13.0 - - - +
36F THR* 4.6 11.2 - - - +
58F GLU* 4.9 9.6 - - + +
59F PHE* 1.3 74.5 - - - +
61F ALA* 1.3 72.4 + - + +
62F GLY 2.9 4.2 + - - -
63F VAL 3.1 14.0 + - - +
65F HIS* 3.4 43.7 - - + +
60M VAL* 4.9 5.6 - - + -
65M HIS* 3.1 23.4 - - + -
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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