Contacts of the helix formed by residues 55 - 62 (chain A) in PDB entry 4QY2
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 HIS 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A CYS* 1.3 78.1 - - - +
56A PRO* 1.3 70.4 - - + +
57A ILE* 3.3 37.4 + - + +
58A GLY* 2.7 30.8 + - - -
79A GLU* 4.2 10.9 + - - -
80A ARG 5.8 0.2 - - - -
83A ALA* 3.5 25.3 - - + +
84A ILE 3.0 29.7 + - - +
85A ALA* 3.6 10.3 - - + +
86A TYR* 6.1 0.2 - - - -
95A VAL* 5.4 4.5 - - + -
99A ARG* 3.9 21.9 - - - -
393B PHE* 6.5 0.2 - - + -
394B SER* 5.5 5.3 + - - -
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Residues in contact with PRO 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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51A LEU* 3.7 17.0 - - + -
54A CYS 3.7 5.8 - - - +
55A HIS* 1.3 98.6 - - + +
57A ILE* 1.3 61.5 + - - +
59A MET* 2.9 33.6 + - + +
60A LEU 3.8 0.7 + - - -
79A GLU* 3.7 26.2 - - + +
99A ARG* 4.4 12.3 - - + -
102A ILE* 3.7 33.6 - - + +
103A MET* 4.0 11.2 - - - -
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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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55A HIS* 3.2 27.0 + - + +
56A PRO* 1.3 77.1 - - - +
58A GLY* 1.3 62.6 + - - +
60A LEU* 3.0 16.8 + - - +
61A ILE* 3.3 24.8 + - + +
85A ALA* 4.2 13.0 - - + -
86A TYR* 4.2 2.7 - - + +
92A THR* 3.8 18.4 - - - +
95A VAL* 4.0 22.2 - - + +
98A LEU* 4.0 18.8 - - + -
99A ARG* 3.8 32.5 - - + +
102A ILE* 4.2 6.7 - - + -
172A MET* 4.7 8.7 - - + -
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Residues in contact with GLY 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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55A HIS 2.7 18.8 + - - -
57A ILE* 1.3 72.8 - - - +
59A MET* 1.3 58.0 + - - -
61A ILE* 4.0 3.1 - - - -
62A GLY* 2.8 27.1 + - - -
63A THR* 3.2 27.6 + - - -
66A CYS* 3.5 14.1 - - - +
85A ALA* 4.2 8.2 - - - +
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Residues in contact with MET 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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49A LYS* 4.9 2.0 - - + -
51A LEU* 3.7 28.0 - - + -
54A CYS* 3.7 19.1 - - - -
55A HIS 3.5 0.6 + - - -
56A PRO* 2.9 27.7 + - + +
58A GLY* 1.3 77.0 - - - +
60A LEU* 1.3 52.4 + - - +
66A CYS* 3.7 4.7 - - - -
69A HIS* 3.3 27.4 - - + +
70A LEU* 3.9 9.9 - - - +
74A TRP* 3.6 34.8 - - + -
77A LEU* 4.6 2.7 - - + -
102A ILE* 4.2 15.0 - - - -
108A ILE* 3.6 13.5 - - + -
110A LYS* 2.7 31.7 + - - -
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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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57A ILE 3.0 8.7 + - - +
59A MET* 1.3 81.1 - - + +
61A ILE* 1.3 58.4 + - - +
98A LEU* 3.9 20.4 - - + -
102A ILE* 3.6 33.7 - - + -
108A ILE* 3.7 30.3 - - + -
110A LYS* 3.7 5.0 + - - +
141A GLU* 3.2 20.3 - - - +
170A LEU* 4.1 17.3 - - + -
172A MET* 3.8 23.3 - - + +
249A ARG 5.3 1.4 - - - +
251A SER* 3.5 26.8 + - - +
253A LEU* 4.5 5.6 - - + -
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Residues in contact with ILE 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 ILE* 3.3 23.5 + - + +
60A LEU* 1.3 76.6 - - - +
62A GLY* 1.3 59.9 + - - +
63A THR* 3.8 7.2 - - - +
85A ALA 3.8 10.8 - - - +
86A TYR* 4.4 1.3 - - + -
139A TYR* 3.2 43.0 - - + +
141A GLU* 3.0 26.5 + - - +
142A LEU* 3.7 25.5 + - + -
172A MET* 3.8 35.7 - - + -
225A PHE* 3.9 22.4 - - + -
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Residues in contact with GLY 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 GLY 2.8 13.8 + - - -
59A MET 4.2 0.2 + - - -
60A LEU 3.5 2.2 - - - -
61A ILE* 1.3 79.2 - - - +
63A THR* 1.3 64.2 + - - -
70A LEU* 3.8 13.2 - - - -
132A ARG* 3.0 10.8 + - - -
139A TYR* 3.6 3.3 - - - -
140A ALA* 2.8 28.4 + - - +
141A GLU* 3.6 12.5 - - - +
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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