Contacts of the helix formed by residues 59 - 69 (chain B) in PDB entry 5EGU
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 GLN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.6 9.3 - - + +
57B LYS* 3.2 23.7 + - - +
58B ARG* 1.3 83.6 - - - +
60B THR* 1.3 66.6 + - - +
61B ASN* 3.3 3.4 - - - -
62B GLN* 3.1 29.8 + - + +
63B LEU* 3.0 20.1 + - - +
121B ASN* 5.4 1.6 - - + -
122B ALA* 4.1 4.0 - - + +
166B THR 4.4 0.9 - - - +
167B GLU* 3.2 18.2 - - + +
168B GLU* 2.6 61.1 + - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 3.7 20.2 - - + +
59B GLN* 1.3 75.0 - - - +
61B ASN* 1.3 63.7 + - - +
63B LEU* 3.2 10.1 + - + +
64B GLN* 3.0 39.3 + - - +
168B GLU 5.7 1.6 + - - -
124D GLU* 3.6 35.4 - - + +
127D GLN* 5.4 7.3 - - - +
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLN 3.3 0.8 - - - -
60B THR* 1.3 82.2 + - - +
62B GLN* 1.3 62.6 + - + +
64B GLN* 3.4 22.6 + - - +
65B TYR* 3.2 22.7 + - - +
165B PRO* 3.9 19.7 - - + +
166B THR 5.3 5.8 + - - +
168B GLU 3.9 20.9 + - - +
127D GLN* 5.3 10.7 + - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLN* 3.1 36.4 + - + +
61B ASN* 1.3 76.0 - - + +
63B LEU* 1.3 60.0 + - - +
65B TYR* 3.3 5.3 + - - +
66B LEU* 2.8 34.2 + - - +
122B ALA* 3.4 17.4 - - + +
123B GLN* 4.9 7.1 + - - +
126B ILE* 5.2 0.2 - - - +
164B LEU* 3.7 34.2 - - + +
165B PRO* 2.9 32.2 + - + +
166B THR 4.7 1.8 - - - +
167B GLU* 3.7 24.1 - - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 3.6 54.5 - - + +
59B GLN 3.0 12.8 + - - +
60B THR* 3.6 10.5 - - + +
62B GLN* 1.3 75.9 - - - +
64B GLN* 1.3 57.7 + - + +
66B LEU* 2.9 20.2 + - - +
67B LEU* 3.0 11.6 + - - +
114B LEU* 3.7 29.9 - - + +
117B ASN* 4.7 3.1 - - - +
119B TYR* 3.9 16.8 - - + -
121B ASN 4.4 2.5 - - - -
122B ALA* 3.7 25.4 - - - +
125B CYS* 4.0 7.9 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 3.0 22.0 + - - +
61B ASN* 3.4 29.5 + - - +
62B GLN 3.3 0.2 - - - -
63B LEU* 1.3 73.2 - - + +
65B TYR* 1.3 58.9 + - - +
67B LEU* 3.2 7.4 + - - +
68B ARG* 2.9 40.2 + - + +
103D THR* 3.4 38.6 + - + +
105D MET* 5.4 4.0 - - - +
113D ARG* 5.6 2.0 - - - +
127D GLN* 6.0 3.6 - - - +
128D ASP* 4.3 16.0 + - - -
131D THR* 5.0 5.7 + - - +
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN 3.2 7.0 + - - +
62B GLN 3.5 7.4 - - - +
64B GLN* 1.3 75.7 - - - +
66B LEU* 1.3 63.1 + - - +
68B ARG* 4.9 1.8 - - - -
69B VAL* 2.9 58.4 + - + +
70B VAL* 3.0 27.0 + - + -
160B LYS* 2.5 38.7 + - - +
161B ILE* 5.0 0.2 - - - -
163B GLU* 3.5 26.3 - - + +
164B LEU* 3.9 15.5 - - + -
165B PRO* 3.4 30.7 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN 2.8 20.5 + - - +
63B LEU* 2.9 12.9 + - - +
65B TYR* 1.3 78.0 - - - +
67B LEU* 1.3 50.9 + - - +
70B VAL* 3.5 17.5 - - + +
71B LEU* 2.7 35.7 + - - +
114B LEU* 3.9 4.7 - - + +
122B ALA* 3.9 31.4 - - + +
125B CYS* 4.0 26.2 - - + -
126B ILE* 4.1 13.0 - - + -
129B PHE* 4.3 17.3 - - + -
161B ILE* 4.0 26.5 - - + -
164B LEU* 4.3 7.6 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 3.0 10.3 + - - +
64B GLN* 3.6 9.0 - - - +
66B LEU* 1.3 75.4 - - - +
68B ARG* 1.3 75.3 + - + +
69B VAL 3.4 0.2 + - - -
71B LEU* 3.4 19.0 - - + +
72B LYS* 3.2 25.1 + - - +
111B LYS* 4.5 12.1 - - + +
114B LEU* 3.7 40.4 - - + +
115B GLU* 4.4 21.3 - - + +
113D ARG* 6.3 0.9 - - - +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLN* 2.9 28.8 + - + +
65B TYR* 4.9 0.7 - - - -
67B LEU* 1.3 84.2 - - + +
69B VAL* 1.3 67.1 + - + +
72B LYS* 3.4 52.1 + - - +
98D TYR* 3.9 22.0 + - - +
101D ILE 5.0 1.6 + - - -
102D LYS 3.6 22.6 + - - +
103D THR* 5.7 1.3 - - + -
104D PRO* 3.6 32.0 - - + +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 2.9 55.3 + - + +
68B ARG* 1.3 88.0 - - + +
70B VAL* 1.3 65.4 - - - +
71B LEU 3.6 0.2 - - - -
73B THR* 2.7 35.9 + - - +
160B LYS* 4.0 21.8 - - + +
102D LYS* 5.5 12.3 - - + -
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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