Contacts of the strand formed by residues 18 - 27 (chain F) in PDB entry 2J0Q
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 GLY 18 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F LYS* 3.3 5.1 - - - -
15F GLY 2.9 32.1 + - - -
16F LYS 3.4 2.0 + - - -
17F PHE* 1.3 79.0 - - - +
19F HIS* 1.3 60.8 - - - -
20F GLU* 3.4 5.3 + - - +
39F ASN* 3.7 15.0 - - - -
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Residues in contact with HIS 19 (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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10F TYR* 3.0 28.4 + + - -
13F HIS 3.4 15.0 - - - -
14F LYS* 3.8 35.0 - - + -
17F PHE 5.1 0.4 - - - -
18F GLY* 1.3 68.9 - - - -
20F GLU* 1.3 62.4 + - - +
21F PHE* 3.4 30.7 - + - -
37F ASN* 2.7 35.5 + - - +
38F SER* 5.2 0.9 - - - -
39F ASN* 4.7 3.2 - - - +
85F ARG* 5.7 1.0 + - - -
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Residues in contact with GLU 20 (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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358B ARG* 2.8 33.6 + - - -
391B ASP 5.4 0.5 - - - +
394B GLN* 2.9 14.8 + - - +
395B TYR* 4.0 3.1 - - - +
13F HIS* 2.8 68.8 + - + +
17F PHE* 3.4 32.2 - - - +
18F GLY 3.4 1.9 + - - +
19F HIS* 1.3 71.0 - - - +
21F PHE* 1.3 59.9 + - - +
37F ASN 3.3 6.1 - - - +
38F SER* 2.7 32.3 + - - +
192I ASP* 3.8 6.4 - - - +
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Residues in contact with PHE 21 (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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394B GLN* 3.4 6.9 - - - +
10F TYR* 3.4 24.9 - + + +
11F VAL 3.3 13.7 - - - +
12F GLY* 3.9 2.0 - - - -
19F HIS* 3.4 40.2 - + - +
20F GLU* 1.3 74.4 - - - +
22F LEU* 1.3 61.8 + - - +
23F GLU* 4.1 27.4 - - + -
35F ALA* 4.6 14.1 - - + -
36F ASN* 3.4 3.7 - - - +
37F ASN* 2.7 67.4 + - + +
45F MET* 4.7 11.9 - - + -
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Residues in contact with LEU 22 (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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394B GLN* 4.1 22.4 - - + +
397B SER* 4.0 13.2 - - - +
9F TYR* 4.5 7.2 - - + -
10F TYR* 3.7 2.1 - - - -
11F VAL* 3.0 38.7 + - + +
21F PHE* 1.3 72.6 - - - +
23F GLU* 1.3 69.0 + - - +
24F PHE* 4.7 7.4 - - + -
34F TYR* 3.6 27.4 - - + -
35F ALA 3.3 12.1 - - - +
36F ASN* 4.3 5.4 - - - +
130F LYS* 4.1 24.2 - - + +
134F PHE* 4.1 22.2 - - + -
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Residues in contact with GLU 23 (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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8F ARG* 3.2 32.3 + - + +
9F TYR 3.3 18.2 - - - +
10F TYR* 4.1 13.7 - - + -
21F PHE* 4.1 26.1 - - + -
22F LEU* 1.3 78.1 - - - +
24F PHE* 1.3 64.7 + - - +
25F GLU* 6.0 0.2 - - + -
33F ARG* 4.8 16.0 + - - +
34F TYR* 3.5 0.9 - - - -
35F ALA* 2.7 42.1 + - + +
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Residues in contact with PHE 24 (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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7F LEU* 4.8 9.9 - - + -
8F ARG* 3.4 4.1 - - - +
9F TYR* 3.0 76.0 + + + +
22F LEU* 4.7 11.0 - - + -
23F GLU* 1.3 76.6 - - - +
25F GLU* 1.3 63.8 + - - +
26F PHE* 4.1 15.9 - + - -
32F LEU* 4.5 1.8 - - + -
33F ARG 3.3 9.6 - - - +
34F TYR* 4.3 8.7 - - + -
129F LEU* 3.8 26.9 - - + -
130F LYS* 4.4 16.4 - - + -
133F VAL* 3.5 46.9 - - + -
134F PHE* 5.9 1.3 - + - -
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Residues in contact with GLU 25 (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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6F TYR* 3.1 40.0 + - + +
7F LEU 3.6 4.0 - - - -
8F ARG* 3.9 16.3 - - + -
23F GLU* 6.0 1.1 - - + -
24F PHE* 1.3 76.1 - - - +
26F PHE* 1.3 65.7 + - - +
27F ARG* 3.2 28.9 + - - +
31F LYS 4.1 1.0 - - - +
32F LEU* 3.3 13.3 - - - +
33F ARG* 2.7 68.4 + - + +
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Residues in contact with PHE 26 (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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5F PHE* 4.3 1.1 - - + +
6F TYR* 3.2 9.5 - - - -
7F LEU* 2.8 44.6 + - + +
24F PHE* 4.1 11.4 - + - -
25F GLU* 1.3 74.8 - - - +
27F ARG* 1.3 64.2 + - - +
31F LYS 3.4 4.0 - - - -
32F LEU* 3.5 33.4 - - + -
52F VAL* 4.5 12.8 - - + -
56F VAL* 4.8 4.3 - - + -
57F MET* 4.2 24.1 - - + +
60F LEU* 3.5 35.2 - - + -
132F LEU* 4.6 5.4 - - + -
133F VAL* 3.6 32.5 - - + -
136F LEU* 4.2 14.1 - - + -
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Residues in contact with ARG 27 (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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5F PHE 3.9 0.4 - - - -
6F TYR* 3.9 9.9 - - + -
25F GLU* 3.2 31.6 - - - +
26F PHE* 1.3 75.1 - - - +
28F PRO* 1.3 77.1 - - + +
29F ASP* 3.2 24.8 + - - +
30F GLY* 3.0 19.2 + - - -
31F LYS* 3.1 56.4 + - + +
33F ARG* 5.3 5.8 - - - +
51F TYR* 5.5 0.8 + - - -
57F MET* 3.4 3.9 - - - +
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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