Contacts of the strand formed by residues 21 - 28 (chain F) in PDB entry 5HHM
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 ARG 21 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F THR 3.8 1.0 - - - +
11F SER* 3.2 6.7 + - - -
12F VAL* 2.8 48.1 + - + +
14F ARG* 3.9 21.9 - - - +
20F PRO* 1.3 72.1 - - - +
22F PHE* 1.3 58.2 + - - +
23F ILE* 3.8 27.0 - - + +
37F ASP* 2.8 35.6 + - - +
38F SER* 3.5 12.3 - - - +
39F ASP* 2.8 43.3 + - - +
54G LEU* 5.9 0.8 - - - +
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Residues in contact with PHE 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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9F PHE* 3.4 35.4 - + + -
10F THR 3.5 11.2 - - - -
11F SER* 4.2 14.4 - - - +
20F PRO 3.8 1.7 + - - +
21F ARG* 1.3 72.2 - - - +
23F ILE* 1.3 62.1 + - - +
24F ALA* 3.9 6.7 - - + -
36F PHE* 3.7 17.0 - + - -
37F ASP* 3.7 5.1 - - - +
38F SER* 3.1 39.6 + - - -
67F VAL* 3.7 30.7 - - + -
70F HIS* 4.0 4.7 - - + -
71F SER* 3.6 42.4 - - - +
74F HIS* 3.4 27.1 - - - -
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Residues in contact with ILE 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 PHE 3.6 1.2 - - - +
9F PHE* 3.3 6.6 - - - +
10F THR* 2.9 54.9 + - + +
12F VAL* 4.8 3.6 - - + -
21F ARG* 3.8 40.6 - - + +
22F PHE* 1.3 78.7 - - - +
24F ALA* 1.3 60.7 + - - +
25F VAL* 4.0 13.5 - - + -
35F ARG* 6.1 0.7 - - + -
36F PHE 3.4 8.5 - - - +
37F ASP* 4.5 7.4 - - + +
53G ASP* 5.3 2.2 - - + -
54G LEU* 3.8 56.5 - - + +
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Residues in contact with ALA 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 TYR* 6.4 1.1 - - + -
8F PHE 3.6 4.7 - - - -
9F PHE* 3.9 18.4 - - + -
22F PHE* 3.9 3.3 - - + -
23F ILE* 1.3 73.6 - - - +
25F VAL* 1.3 64.2 + - - +
35F ARG* 3.1 5.8 - - - +
36F PHE* 2.8 41.8 + - + +
45F MET* 4.9 5.8 - - + -
67F VAL* 3.6 31.6 - - + -
2H ILE* 6.5 0.2 - - + -
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Residues in contact with VAL 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 ARG 4.0 0.5 - - - +
7F TYR* 3.5 7.1 - - - -
8F PHE* 2.9 55.8 + - + +
9F PHE* 6.0 0.2 - - - -
23F ILE* 4.0 6.7 - - + -
24F ALA* 1.3 81.3 - - - +
26F GLY* 1.3 58.0 + - - +
27F TYR* 3.9 18.8 - - + -
32F GLN* 3.8 13.7 - - - +
34F VAL* 3.4 7.0 - - - +
35F ARG* 4.3 1.8 - - + -
53G ASP* 3.8 26.5 - - + +
54G LEU 3.6 26.7 - - - +
55G SER* 4.0 4.3 - - - -
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Residues in contact with GLY 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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6F ARG 3.4 6.3 - - - -
7F TYR* 3.6 20.6 - - - -
25F VAL* 1.3 74.1 - - - +
27F TYR* 1.3 56.9 + - - -
32F GLN* 3.3 6.2 - - - +
33F PHE* 2.7 37.4 + - - -
34F VAL* 3.1 17.4 + - - +
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Residues in contact with TYR 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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4F SER 4.0 0.2 - - - +
5F MET* 3.3 3.8 - - - -
6F ARG* 2.8 44.4 + - + +
8F PHE* 3.7 21.3 - + + -
25F VAL* 3.9 14.8 - - + -
26F GLY* 1.3 76.2 - - - -
28F VAL* 1.3 57.7 + - - +
29F ASP 3.8 13.5 - - - +
30F ASP* 3.9 17.7 - - - -
31F THR 3.5 7.0 - - - -
32F GLN* 3.4 45.8 + - + +
33F PHE* 3.5 10.9 - - - -
53G ASP 4.7 1.9 + - - -
55G SER* 3.5 26.5 - - - -
63G TYR* 3.4 25.9 + + - -
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Residues in contact with VAL 28 (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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4F SER 3.4 3.4 - - - -
5F MET* 4.6 2.5 - - + -
27F TYR* 1.3 69.5 - - - +
29F ASP* 1.3 67.5 + - - +
31F THR* 3.0 28.7 + - - +
33F PHE* 3.7 25.5 - - + -
51F TRP* 3.8 9.9 - - + -
168F LEU* 3.8 22.7 - - + -
171F TYR* 3.7 24.7 - - + -
172F LEU* 3.9 12.3 - - + -
179F LEU* 3.8 32.2 - - + +
209F TYR* 4.0 0.5 + - - -
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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