Contacts of the helix formed by residues 53 - 62 (chain A) in PDB entry 2FHP
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 2.7 31.5 + - - -
51A GLY 3.1 0.6 - - - -
52A SER* 1.3 79.5 + - - +
54A GLY* 1.3 64.1 + - - +
55A LEU 3.2 3.0 + - - -
56A ALA* 3.3 4.7 + - - +
57A ILE* 3.0 32.3 + - - +
80A ILE* 3.6 12.1 - - - -
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.6 25.0 - - - +
3A VAL* 6.1 0.2 - - - +
13A LEU* 4.1 8.6 - - - +
29A LYS* 3.8 15.7 + - - +
50A SER 4.4 1.0 + - - -
52A SER* 3.5 4.8 + - - -
53A GLY* 1.3 78.0 - - - +
55A LEU* 1.3 57.5 + - - +
57A ILE* 3.5 2.3 + - - +
58A GLU* 3.0 28.4 + - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.1 18.6 - - + +
29A LYS* 3.8 30.5 - - + -
32A ILE* 4.8 6.1 - - + -
33A PHE* 3.5 18.2 - - + -
47A ASP* 4.0 11.8 + - - +
50A SER 5.6 0.2 + - - -
53A GLY 3.3 0.4 - - - -
54A GLY* 1.3 73.3 - - - +
56A ALA* 1.3 66.6 + - - +
58A GLU* 3.2 4.0 + - - -
59A ALA* 3.0 20.3 + - - +
118A LEU* 3.9 37.9 - - + -
120A ASP* 4.9 9.2 - - + +
148A VAL* 6.2 0.2 - - + -
150A GLU* 3.4 23.1 - - + +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 5.7 0.2 - - - -
47A ASP* 3.2 25.2 + - + +
50A SER* 4.2 0.2 - - - +
53A GLY 3.3 7.1 + - - +
55A LEU* 1.3 77.2 - - - +
57A ILE* 1.3 62.6 + - - +
59A ALA* 3.3 3.7 + - - +
60A VAL* 3.2 15.9 + - - +
67A SER* 3.0 29.4 + - - -
69A CYS* 3.4 30.1 - - - -
93A PHE* 4.0 4.7 - - + -
118A LEU* 4.7 2.7 - - - -
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.8 27.6 - - + -
8A TYR* 4.0 4.8 - - + -
13A LEU* 4.1 9.2 - - + -
52A SER 4.5 0.9 - - - +
53A GLY* 3.0 26.7 + - - +
54A GLY* 3.9 4.5 - - - +
56A ALA* 1.3 76.1 - - + +
58A GLU* 1.3 60.5 + - - +
60A VAL* 3.4 1.7 + - - +
61A SER* 2.8 28.2 + - - -
80A ILE* 5.5 0.4 - - + -
83A ASN* 3.6 43.1 - - + +
84A ILE* 4.1 6.7 - - + +
87A THR* 3.8 20.2 - - + -
93A PHE* 3.8 24.7 - - + -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.4 12.1 - - - +
4A ILE* 2.9 29.6 + - - +
5A SER 2.9 21.8 + - - +
29A LYS* 3.7 15.5 + - + -
33A PHE* 3.5 26.5 - - + -
54A GLY 3.0 16.6 + - - +
55A LEU 3.2 5.6 + - - +
57A ILE* 1.3 78.4 - - - +
59A ALA* 1.3 61.3 + - - +
61A SER* 3.3 4.5 + - - -
62A ARG* 2.8 62.1 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PHE* 3.7 20.1 - - + -
40A PHE* 3.8 4.4 - - - -
45A ALA* 4.2 7.2 - - + -
55A LEU 3.0 12.5 + - - +
56A ALA* 3.5 9.4 - - - +
57A ILE 3.2 0.2 - - - -
58A GLU* 1.3 75.9 - - - +
60A VAL* 1.3 62.5 + - - +
62A ARG* 3.3 4.2 + - - -
63A GLY 3.3 6.4 + - - -
64A MSE 3.1 28.2 + - + +
67A SER* 4.1 9.0 - - - +
116A LEU* 3.9 18.2 - - + -
118A LEU* 5.0 0.4 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU* 5.5 1.9 - - - +
8A TYR* 3.5 23.9 + - + +
56A ALA 3.2 5.8 + - - +
57A ILE 4.0 0.4 - - - +
59A ALA* 1.3 72.2 - - - +
61A SER* 1.3 67.5 + - - +
63A GLY* 3.0 13.5 + - - -
64A MSE 3.4 22.8 - - + +
66A LYS* 4.0 4.3 - - - -
67A SER* 3.3 35.9 - - - +
92A LYS* 3.7 23.7 + - + +
93A PHE* 3.7 26.7 - - + -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.6 11.0 - - - +
5A SER 2.6 26.3 + - - -
6A GLY* 3.2 3.4 - - - -
7A GLU* 2.9 30.7 + - - +
8A TYR* 2.9 42.4 + - - -
57A ILE 2.8 22.7 + - - -
58A GLU 3.5 4.3 - - - -
60A VAL* 1.3 74.9 - - - +
62A ARG* 1.3 57.0 + - - +
63A GLY* 3.4 3.1 + - - -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.8 12.3 - - - +
5A SER* 3.4 35.8 + - - +
30A GLU* 4.5 5.1 - - - +
33A PHE* 3.4 36.6 - - - +
34A ASN* 3.0 29.9 + - - -
38A PRO* 2.9 36.5 + - - +
39A TYR* 3.3 24.3 - - + +
40A PHE* 2.8 33.4 + - + +
58A GLU* 2.8 43.9 + - - +
59A ALA 3.6 6.5 - - - +
60A VAL 3.1 0.4 - - - -
61A SER* 1.3 74.3 - - - +
63A GLY* 1.3 57.3 + - - +
64A MSE 3.8 0.2 - - - -
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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