Contacts of the helix formed by residues 48 - 60 (chain A) in PDB entry 1GC5
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 ASP 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TYR 3.5 4.6 + - - +
47A LEU* 1.3 75.0 - - - +
49A ALA* 1.3 69.4 + - - +
50A ASP* 3.6 18.4 + - - +
51A ASP* 2.9 40.8 + - + +
52A LEU* 2.9 22.0 + - - +
193A PHE* 3.7 2.9 - - - -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 1.3 72.2 + - - +
50A ASP* 1.3 57.4 + - - +
52A LEU* 3.1 0.9 + - - -
53A GLU* 2.7 44.9 + - - +
193A PHE* 3.3 20.4 - - + -
194A GLN* 3.0 31.6 - - + +
195A VAL* 4.1 4.3 - - - -
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Residues in contact with ASP 50 (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 ASP* 3.3 15.4 + - - +
49A ALA* 1.3 81.1 - - - +
51A ASP* 1.3 54.6 + - - +
53A GLU* 3.3 6.0 + - - -
54A LYS* 2.7 67.3 + - - +
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Residues in contact with ASP 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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45A LYS* 4.6 3.5 + - - +
48A ASP* 2.9 33.3 + - + +
50A ASP* 1.3 76.9 - - - +
52A LEU* 1.3 52.1 + - - +
54A LYS* 3.3 6.1 + - - +
55A ARG* 2.7 61.0 + - - +
111A TRP* 2.8 32.4 + - - -
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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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47A LEU* 4.0 26.2 - - + -
48A ASP 2.9 15.8 + - - +
49A ALA 3.8 5.4 - - - +
51A ASP* 1.3 74.3 + - - +
53A GLU* 1.3 53.4 + - - +
55A ARG* 4.1 4.3 - - + +
56A VAL* 2.7 57.8 + - + +
82A LEU* 4.1 22.9 - - + -
85A ILE* 4.1 13.2 - - + -
86A LEU* 3.6 26.7 - - + -
89A ILE* 4.4 0.9 - - + -
111A TRP* 4.1 15.5 - - + -
193A PHE* 4.3 0.9 - - + -
195A VAL* 4.0 18.2 - - + -
196A PHE* 4.2 0.7 - - - -
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Residues in contact with GLU 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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49A ALA* 2.7 31.7 + - - +
50A ASP* 3.3 8.7 - - - +
52A LEU* 1.3 75.4 - - - +
54A LYS* 1.3 67.7 + - + +
55A ARG 3.0 1.4 + - - -
56A VAL 3.0 7.6 + - - -
57A THR* 3.0 20.7 + - + +
194A GLN 4.0 4.6 - - - +
195A VAL* 3.2 31.5 - - - +
196A PHE* 3.2 43.7 + - + -
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Residues in contact with LYS 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 ASP* 2.7 59.5 + - - +
51A ASP* 3.7 6.3 - - - +
53A GLU* 1.3 75.8 - - + +
55A ARG* 1.3 59.9 + - + +
57A THR* 2.9 22.9 + - - -
58A GLU* 3.3 20.6 + - - +
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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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51A ASP* 2.7 42.4 + - - +
52A LEU* 3.5 10.1 - - + +
54A LYS* 1.3 73.5 - - + +
56A VAL* 1.3 65.6 + - - +
58A GLU* 3.3 28.2 + - - +
59A LYS* 3.6 5.5 + - - +
82A LEU* 3.8 12.4 - - + +
107A TYR* 3.3 36.5 + - - +
110A GLU 5.3 0.8 + - - -
111A TRP* 3.0 65.8 + - - +
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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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52A LEU* 2.7 45.6 + - + +
55A ARG* 1.3 70.4 - - - +
57A THR* 1.3 65.6 + - - +
58A GLU 3.2 0.5 + - - -
59A LYS* 3.4 4.5 + - - +
60A GLY 2.9 17.7 + - - -
61A LYS* 3.2 30.7 + - + -
64A VAL* 3.5 22.6 - - + +
65A PHE* 4.2 1.6 - - + -
82A LEU* 4.2 16.6 - - + -
86A LEU* 4.2 7.9 - - + -
196A PHE* 2.9 35.4 - - + -
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Residues in contact with THR 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 GLU* 3.0 17.7 + - + +
54A LYS* 2.9 16.3 + - - -
56A VAL* 1.3 74.4 - - - +
58A GLU* 1.3 75.0 + - - +
60A GLY* 2.8 15.1 + - - -
61A LYS* 4.1 18.8 - - + +
196A PHE* 4.1 13.2 - - + -
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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 LYS* 3.3 16.1 + - - +
55A ARG* 3.3 26.0 + - - +
56A VAL 3.1 0.4 - - - -
57A THR* 1.3 85.2 + - - +
59A LYS* 1.3 75.5 + - + +
60A GLY* 4.0 0.3 - - - -
107A TYR* 5.2 3.8 + - - -
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Residues in contact with LYS 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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55A ARG 3.8 4.5 - - - +
56A VAL 3.4 4.3 + - - +
58A GLU* 1.3 87.6 - - - +
60A GLY* 1.3 59.4 + - - +
63A LYS* 5.9 3.8 - - - +
64A VAL* 4.5 11.7 - - + -
78A ILE* 2.9 58.6 - - + +
79A GLU* 4.6 14.7 - - + +
82A LEU* 3.7 23.3 - - + -
103A GLU* 5.5 0.2 + - - -
107A TYR* 3.4 20.9 - - - -
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Residues in contact with GLY 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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56A VAL 2.9 5.4 + - - -
57A THR 2.8 14.5 + - - -
58A GLU 4.0 0.2 - - - -
59A LYS* 1.3 82.3 - - - +
61A LYS* 1.3 53.5 + - - -
62A GLU* 2.4 28.5 + - - +
63A LYS* 3.5 10.4 + - - +
64A VAL* 3.3 13.3 + - - +
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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