Contacts of the helix formed by residues 50 - 59 (chain A) in PDB entry 1EGE
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 VAL 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 2.9 39.2 + - + +
49A PRO* 1.3 69.0 - - - +
51A PRO* 1.4 72.0 - - + +
52A LEU 3.1 0.7 + - - -
53A ILE* 3.1 9.2 + - - +
54A ARG* 2.9 55.6 + - + +
172A LYS* 6.2 0.9 - - + -
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Residues in contact with PRO 51 (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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42A TYR* 4.4 18.6 - - + +
47A GLU* 5.9 1.3 - - - +
48A TYR 4.7 2.0 - - - +
49A PRO* 3.6 3.8 - - + -
50A VAL* 1.4 92.8 - - + +
52A LEU* 1.3 59.3 + - + +
54A ARG* 3.7 24.0 - - + +
55A ARG* 3.1 28.8 + - - +
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Residues in contact with LEU 52 (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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30A PHE* 3.5 13.6 - - + -
34A GLU* 4.2 18.4 - - + +
35A ILE* 4.3 16.6 - - + +
38A VAL* 3.8 24.2 - - + -
42A TYR* 3.8 32.5 - - + +
49A PRO* 2.8 20.5 + - + +
51A PRO* 1.3 73.8 - - + +
53A ILE* 1.3 59.7 + - - +
55A ARG* 3.2 3.9 + - + -
56A ALA* 2.8 29.2 + - - +
94A VAL* 3.9 33.7 - - + -
98A ILE* 5.4 0.2 - - - -
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Residues in contact with ILE 53 (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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48A TYR* 3.3 46.0 - - + +
49A PRO* 3.4 30.1 - - + +
50A VAL* 3.1 6.4 + - - +
52A LEU* 1.3 74.4 - - + +
54A ARG* 1.3 63.7 + - - +
56A ALA* 2.9 9.1 + - - +
57A TRP* 2.9 19.8 + - - +
62A MET* 3.2 36.0 - - + +
94A VAL* 5.1 1.5 - - + +
97A ALA* 4.3 5.6 - - + -
98A ILE* 4.1 19.5 - - + -
130A MET* 3.8 16.2 - - + -
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Residues in contact with ARG 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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50A VAL* 2.9 44.6 + - + +
51A PRO* 3.7 20.9 - - - +
53A ILE* 1.3 75.5 - - - +
55A ARG* 1.3 51.6 + - - +
57A TRP* 2.8 18.6 + - + +
58A GLU* 2.8 35.9 + - + +
128A PRO* 4.7 24.5 - - + -
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Residues in contact with ARG 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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30A PHE* 3.4 22.4 - - + -
34A GLU* 3.2 25.9 + - - +
51A PRO 3.1 16.6 + - - +
52A LEU* 3.2 5.6 + - + +
54A ARG* 1.3 78.2 - - - +
56A ALA* 1.3 56.2 + - - +
58A GLU* 2.8 38.4 + - - -
59A LEU* 2.8 84.5 + - - +
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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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30A PHE* 4.0 17.0 - - + -
52A LEU 2.8 13.9 + - - +
53A ILE 2.9 11.0 + - - +
55A ARG* 1.3 76.0 - - - +
57A TRP* 1.3 54.9 + - - +
59A LEU* 3.1 4.6 + - - +
60A GLY 2.8 28.2 + - - -
61A LEU* 2.9 21.7 + - + -
62A MET* 4.3 7.9 - - + -
98A ILE* 3.9 24.9 - - + -
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Residues in contact with TRP 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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53A ILE 2.9 10.7 + - - +
54A ARG* 2.8 13.6 + - + +
56A ALA* 1.3 74.1 - - - +
58A GLU* 1.3 87.4 + - + +
60A GLY* 3.0 17.2 + - - -
62A MET* 3.6 36.3 - - + +
63A ASN* 4.2 7.6 - - + -
124A MET 3.3 22.3 + - - -
125A THR* 3.2 24.1 + - - +
126A GLU 4.0 9.6 - - - -
127A GLU* 5.4 0.4 - - - -
128A PRO* 3.7 48.2 - - + +
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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 ARG* 2.8 17.1 + - + +
55A ARG* 2.8 42.5 + - - +
57A TRP* 1.3 92.8 - - + +
59A LEU* 1.3 59.5 + - - +
60A GLY* 3.0 5.8 + - - -
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Residues in contact with LEU 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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26A THR* 3.7 21.6 - - + +
29A LYS* 6.5 1.3 - - + -
30A PHE* 3.6 37.9 - - + -
34A GLU* 5.0 0.2 - - - +
55A ARG* 2.8 55.1 + - - +
56A ALA* 4.4 0.4 - - - -
58A GLU* 1.3 76.1 - - - +
60A GLY* 1.3 61.4 + - - +
61A LEU* 3.3 23.1 - - + +
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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