Contacts of the helix formed by residues 61 - 78 (chain Q) in PDB entry 5GJQ
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 61 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q LEU* 1.5 42.1 + - - +
59Q LYS* 2.6 11.5 - - - -
60Q THR* 1.3 67.9 - - - +
62Q GLN* 1.3 52.8 + - - -
63Q ALA 3.0 0.4 - - - -
64Q ALA* 2.9 19.2 + - - +
65Q GLU 2.3 32.6 + - - -
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Residues in contact with GLN 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Q LEU* 4.2 4.3 - - + +
56Q LEU* 2.7 13.5 - - - -
57Q LEU* 3.8 22.4 - - + +
60Q THR 4.5 1.1 - - - +
61Q GLY* 1.3 76.8 - - - +
63Q ALA* 1.3 50.0 + - - +
65Q GLU* 3.1 5.6 - - - +
66Q LEU* 2.2 40.6 + - - +
92Q LEU* 5.3 6.6 - - + +
96Q PHE* 3.7 35.2 - - + -
109Q LEU* 4.6 0.5 - - - +
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Residues in contact with ALA 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q THR* 2.9 18.8 + - - +
62Q GLN* 1.3 75.3 - - - +
64Q ALA* 1.3 66.7 + - - +
66Q LEU* 3.1 20.0 - - - +
67Q GLY 3.5 2.8 + - - -
105Q GLN* 2.9 42.3 + - - +
109Q LEU* 5.5 0.2 - - - -
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Residues in contact with ALA 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q GLY* 2.9 24.0 + - - +
63Q ALA* 1.3 82.7 - - - +
65Q GLU* 1.3 60.2 + - - +
66Q LEU 3.0 0.2 + - - -
67Q GLY* 3.2 2.6 + - - -
68Q GLY* 3.2 14.6 + - - -
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Residues in contact with GLU 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q LEU* 5.3 3.8 - - + -
56Q LEU* 4.0 9.9 - - + -
61Q GLY 2.3 28.9 + - - +
62Q GLN* 3.6 9.2 - - - +
64Q ALA* 1.3 67.0 - - - +
66Q LEU* 1.3 52.2 + - - +
68Q GLY* 2.8 5.6 + - - +
69Q LEU* 2.3 40.0 + - - +
92Q LEU* 4.7 14.6 - - + -
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Residues in contact with LEU 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q GLN 2.2 28.9 + - - +
63Q ALA* 3.1 17.0 - - - +
65Q GLU* 1.3 64.4 - - - +
67Q GLY* 1.3 60.0 + - - +
69Q LEU* 2.9 29.6 + - - +
70Q LEU* 3.7 1.9 + - - +
92Q LEU* 5.3 2.6 - - - +
105Q GLN* 5.2 1.6 - - + -
109Q LEU* 2.7 49.3 - - + +
112Q GLU* 4.6 7.2 - - - +
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Residues in contact with GLY 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Q ALA 3.5 2.8 + - - -
64Q ALA 3.2 6.4 + - - -
66Q LEU* 1.3 79.7 - - - +
68Q GLY* 1.3 61.1 + - - +
70Q LEU* 3.2 22.4 + - - +
71Q LYS* 3.7 2.8 + - - +
109Q LEU* 4.8 2.0 - - - +
112Q GLU* 5.6 2.9 - - - -
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Residues in contact with GLY 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q ALA 3.2 9.5 + - - -
65Q GLU* 2.8 10.6 + - - -
67Q GLY* 1.3 72.6 - - - +
69Q LEU* 1.3 54.3 + - - +
71Q LYS* 2.6 16.0 + - - +
72Q TYR* 2.5 38.5 + - - +
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Residues in contact with LEU 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q GLU 2.3 23.0 + - - +
66Q LEU* 2.9 16.4 + - - +
68Q GLY* 1.3 67.8 - - - +
70Q LEU* 1.3 60.5 + - - +
72Q TYR* 3.8 7.9 - - - +
73Q VAL* 2.9 23.7 + - - +
92Q LEU* 4.0 31.0 - - + -
109Q LEU* 5.7 1.6 - - + -
112Q GLU* 6.0 0.4 - - - +
113Q CYS* 5.2 12.1 - - - -
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Residues in contact with LEU 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q LEU 3.7 2.8 + - - +
67Q GLY* 3.2 14.6 + - - +
68Q GLY 3.2 0.2 - - - -
69Q LEU* 1.3 76.5 - - - +
71Q LYS* 1.3 61.9 + - - +
73Q VAL* 3.1 20.5 - - - +
74Q ARG* 3.2 8.3 + - - +
112Q GLU* 5.5 7.9 + - - +
113Q CYS* 6.1 0.8 - - - -
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Residues in contact with LYS 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Q GLY 3.7 1.5 + - - +
68Q GLY* 2.6 23.0 + - - +
70Q LEU* 1.3 73.2 - - - +
72Q TYR* 1.3 53.6 + - - +
74Q ARG* 2.8 12.1 + - - +
75Q PRO* 2.5 36.1 - - - +
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Residues in contact with TYR 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q GLY 2.5 18.8 + - - +
69Q LEU* 3.8 9.9 - - - +
71Q LYS* 1.3 71.0 - - - +
73Q VAL* 1.3 50.5 + - - +
75Q PRO* 3.2 10.5 - - - +
76Q PHE* 2.4 38.7 + - - +
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Residues in contact with VAL 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q LEU 2.9 13.9 + - - +
70Q LEU* 3.1 15.3 - - - +
72Q TYR* 1.3 75.7 - - - +
74Q ARG* 1.3 50.6 + - - +
76Q PHE* 3.0 5.6 + - - +
77Q LEU* 2.4 37.9 + - - +
85Q ALA* 6.4 1.6 - - - -
89Q VAL* 6.0 6.7 - - + -
116Q TRP* 4.7 22.9 - - + +
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Residues in contact with ARG 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q LEU 3.2 7.4 + - - +
71Q LYS* 2.8 16.1 + - - +
73Q VAL* 1.3 75.9 - - - +
75Q PRO* 1.3 55.3 - - - +
77Q LEU* 3.1 12.8 - - - +
78Q ASN* 3.0 27.9 + - - +
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Residues in contact with PRO 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q GLU 5.3 0.7 - - - +
71Q LYS 2.5 17.5 - - - +
72Q TYR* 2.8 17.5 - - - +
74Q ARG* 1.3 71.4 - - - +
76Q PHE* 1.3 62.2 + - - -
77Q LEU 3.1 0.7 - - - -
78Q ASN* 3.6 4.9 + - + +
79Q SER* 3.5 21.3 + - - -
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Residues in contact with PHE 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q ALA* 6.3 2.0 - - - -
72Q TYR 2.4 23.6 + - - +
73Q VAL* 3.7 5.6 - - - +
75Q PRO* 1.3 69.7 - - - +
77Q LEU* 1.3 57.1 + - - +
79Q SER* 2.9 4.4 + - - -
80Q ILE* 2.2 72.3 + - + +
81Q SER 4.9 2.2 - - - +
84Q LYS 5.5 0.4 - - - -
85Q ALA* 5.2 12.8 - - + -
88Q LEU* 5.6 7.2 - - + -
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Residues in contact with LEU 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q VAL 2.4 27.7 + - - +
74Q ARG* 3.1 19.3 - - - +
75Q PRO 3.1 0.4 - - - -
76Q PHE* 1.3 73.7 - - - +
78Q ASN* 1.3 54.4 + - - +
79Q SER 3.3 0.7 + - - -
80Q ILE 4.1 4.3 - - - +
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Residues in contact with ASN 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q GLU* 4.2 8.9 - - - +
74Q ARG 3.0 14.5 + - - +
75Q PRO* 3.6 4.9 + - + +
76Q PHE 3.1 0.4 - - - -
77Q LEU* 1.3 75.2 - - - +
79Q SER* 1.3 60.8 + - - +
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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