Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 2FRV
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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52A ALA* 1.3 72.0 - - - +
54A HIS* 1.3 62.6 + - - -
56A VAL* 3.0 21.4 - - - +
57A GLU* 3.5 3.3 + - - +
10B VAL 5.2 1.6 - - - -
11B VAL* 3.7 8.0 - - - +
12B ASP 3.7 29.6 - - - -
13B PRO* 2.8 23.3 + - - +
174B TYR* 4.8 0.4 - - - -
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Residues in contact with HIS 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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52A ALA 3.5 0.4 + - - -
53A GLY* 1.3 71.0 - - - -
55A ALA* 1.3 62.6 + - - +
57A GLU* 3.8 12.0 - - - +
58A GLU* 3.1 41.6 + - - +
10B VAL* 4.4 29.9 + - + +
12B ASP 5.2 7.4 + - - -
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Residues in contact with ALA 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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51A GLY* 4.6 1.3 - - - -
52A ALA 3.3 15.7 + - - +
53A GLY 3.2 2.2 + - - -
54A HIS* 1.3 76.2 - - - +
56A VAL* 1.3 60.9 + - - +
58A GLU* 3.7 5.6 + - - -
59A ALA* 3.4 5.4 + - - +
171B THR 4.8 0.2 - - - +
172B ASN* 2.5 60.9 + - + +
174B TYR* 4.4 12.3 - - + -
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Residues in contact with VAL 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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44A TYR* 3.5 18.5 - - + -
49A MET* 3.8 23.3 - - + -
51A GLY* 3.2 34.3 - - - +
53A GLY 3.0 26.9 + - - +
55A ALA* 1.3 75.7 - - - +
57A GLU* 1.3 72.9 + - - +
58A GLU 3.3 0.4 - - - -
59A ALA* 3.1 7.8 - - - +
60A LEU 2.9 23.9 + - - -
13B PRO* 3.7 17.5 - - + -
15B THR* 3.9 9.0 - - + -
171B THR 5.1 3.8 - - - +
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Residues in contact with GLU 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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44A TYR* 2.8 31.5 + - - -
53A GLY 3.5 5.1 + - - +
54A HIS* 3.3 15.9 + - - +
56A VAL* 1.3 75.4 - - - +
58A GLU* 1.3 59.7 + - - +
60A LEU* 4.1 16.2 - - - +
61A HIS* 3.0 28.4 + - - +
87A VAL* 4.3 12.2 - - - +
88A GLY* 5.8 4.2 - - - -
90A ARG* 6.0 2.4 + - - -
95A ILE* 5.7 4.0 - - - +
12B ASP 4.4 4.9 - - - +
13B PRO* 3.4 29.1 - - + +
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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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54A HIS* 3.1 35.1 + - - +
55A ALA* 3.8 8.4 - - - +
57A GLU* 1.3 75.7 - - - +
59A ALA* 1.3 56.2 + - - +
61A HIS* 3.4 7.9 + - - +
62A GLU* 3.1 36.2 + - + +
172B ASN* 4.0 9.0 + - - +
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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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43A ASP 4.5 14.5 - - - +
44A TYR* 4.8 1.1 - - + -
49A MET* 4.6 6.3 - - + -
55A ALA 3.4 12.4 + - - +
56A VAL* 3.1 13.7 + - - +
58A GLU* 1.3 76.4 - - - +
60A LEU* 1.3 66.9 + - - +
62A GLU* 4.2 4.1 - - - +
63A ALA* 2.9 27.0 + - - +
171B THR* 4.2 20.4 - - + +
172B ASN* 3.9 8.7 - - - +
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Residues in contact with LEU 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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10A VAL* 3.2 36.1 - - + -
12A LEU* 4.2 12.8 - - + -
44A TYR* 3.6 45.0 - - + -
56A VAL 2.9 11.1 + - - +
57A GLU* 4.1 19.7 - - - +
58A GLU 3.4 0.2 - - - -
59A ALA* 1.3 80.5 - - - +
61A HIS* 1.3 64.3 + - - +
63A ALA* 3.0 9.3 + - - +
64A ILE* 3.1 30.0 + - + +
90A ARG* 6.1 1.3 - - - +
95A ILE* 4.3 15.5 - - + -
98A GLU* 6.5 0.4 - - - -
99A VAL* 4.4 6.7 - - + -
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Residues in contact with HIS 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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57A GLU 3.0 19.1 + - - +
58A GLU* 3.5 7.6 - - - +
59A ALA 3.2 0.2 - - - -
60A LEU* 1.3 77.6 - - - +
62A GLU* 1.3 84.1 + - - +
64A ILE* 3.6 18.1 - - - +
65A LYS* 3.5 33.5 + - - +
98A GLU* 4.8 11.4 + - - -
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Residues in contact with GLU 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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58A GLU* 3.1 19.8 + - + +
59A ALA* 4.2 4.3 - - - +
61A HIS* 1.3 87.3 - - - +
63A ALA* 1.3 67.4 + - - +
64A ILE 3.2 0.2 - - - -
65A LYS* 2.9 52.6 + - - +
66A GLY 4.2 1.6 + - - -
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Residues in contact with ALA 63 (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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8A SER* 4.7 3.5 + - - +
10A VAL* 3.7 23.8 - - + -
43A ASP* 4.0 22.4 - - + +
59A ALA 2.9 20.3 + - - +
60A LEU* 3.6 3.6 - - - +
62A GLU* 1.3 79.1 - - - +
64A ILE* 1.3 58.2 + - - +
65A LYS 3.2 4.0 + - - -
66A GLY* 3.2 12.5 + - - -
68A PHE* 3.8 12.7 - - - +
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Residues in contact with ILE 64 (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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10A VAL* 4.2 5.6 - - + -
60A LEU* 3.1 36.1 + - + +
61A HIS* 3.6 21.8 - - - +
63A ALA* 1.3 74.1 - - - +
65A LYS* 1.3 63.0 + - + +
66A GLY 3.2 2.9 + - - +
68A PHE* 3.5 37.3 - - + -
98A GLU* 3.7 28.9 - - + +
99A VAL* 3.9 25.4 - - + -
102A LYS* 3.9 29.2 - - + +
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Residues in contact with LYS 65 (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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61A HIS* 3.5 40.6 + - - +
62A GLU* 2.9 42.6 + - - +
63A ALA 3.1 1.2 - - - -
64A ILE* 1.3 79.4 - - + +
66A GLY* 1.3 56.1 + - - +
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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