Contacts of the helix formed by residues 57 - 74 (chain B) in PDB entry 5GQQ
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 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 2.6 13.7 + - - +
56B MET* 1.3 79.8 - - - +
58B TRP* 1.3 61.9 + - - +
59B ASP* 3.4 11.3 + - - +
60B SER* 3.0 30.7 + - - +
61B ALA* 2.8 20.1 + - - +
105B ILE* 4.7 0.2 - - - -
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Residues in contact with TRP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MET 3.6 5.9 + - - -
57B ASP* 1.3 71.5 + - - +
59B ASP* 1.3 90.9 + - - +
61B ALA* 3.2 1.6 + - - +
62B ILE* 2.9 55.5 + - + +
91B SER* 2.9 21.8 + - - -
93B VAL* 4.0 15.9 - - + +
105B ILE* 3.7 30.6 - - + +
146B SER* 3.6 20.9 - - - -
147B SER* 3.9 9.0 - - - -
148B ALA* 3.8 25.7 - - + +
151B ASN* 3.4 29.8 - - - -
174B TYR* 5.2 3.6 - - - -
176B THR* 3.4 22.8 - - - +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.3 8.7 + - - +
58B TRP* 1.3 98.1 - - - +
60B SER* 1.3 60.8 + - - +
62B ILE* 3.7 7.9 + - - +
63B GLN* 3.4 17.7 + - - +
146B SER 3.8 5.4 - - - +
147B SER* 3.5 18.0 - - - -
148B ALA* 3.6 20.1 + - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 5.3 1.1 + - - -
57B ASP* 3.0 34.5 + - - +
59B ASP* 1.3 73.6 - - - +
61B ALA* 1.3 67.0 + - - +
62B ILE 3.1 1.3 - - - -
63B GLN* 2.9 22.5 + - - +
64B THR* 2.9 21.1 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 4.2 18.8 - - + +
55B SER* 4.2 13.4 + - - -
57B ASP 2.8 19.7 + - - +
58B TRP 3.6 4.0 - - - +
60B SER* 1.3 73.2 + - - +
62B ILE* 1.3 58.1 + - - +
64B THR* 3.9 6.1 - - - -
65B GLY 3.0 24.1 + - - -
105B ILE* 3.7 28.3 - - + -
107B ILE* 3.3 11.9 - - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 2.9 56.1 + - + +
59B ASP* 3.7 9.2 - - - +
61B ALA* 1.3 78.5 - - - +
63B GLN* 1.3 58.6 + - - +
66B PHE* 3.0 30.2 + - + +
89B VAL* 4.7 11.9 - - + +
90B THR 5.0 0.4 - - - +
91B SER* 4.2 17.0 - - - +
105B ILE* 5.5 0.7 - - + -
107B ILE* 4.2 20.7 - - + +
176B THR* 5.2 0.9 - - - +
182B PRO* 4.6 21.3 - - + -
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP 3.4 9.1 + - - +
60B SER* 2.9 15.6 + - - +
62B ILE* 1.3 81.8 - - + +
64B THR* 1.3 67.4 + - - +
66B PHE* 3.4 4.1 + - - +
67B THR* 3.1 32.6 + - - +
182B PRO* 6.0 3.1 - - + -
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 4.7 13.7 - - + -
60B SER* 2.9 21.6 + - - -
61B ALA* 3.9 6.4 - - - -
63B GLN* 1.3 80.9 + - - +
65B GLY* 1.3 64.6 + - - +
66B PHE 3.5 0.2 + - - -
67B THR* 3.6 5.3 + - - -
68B LYS* 3.3 44.0 + - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.5 22.4 + - - -
53B VAL* 4.6 4.0 - - - +
61B ALA 3.0 14.7 + - - -
64B THR* 1.3 82.0 - - - +
66B PHE* 1.3 61.7 + - - +
68B LYS* 3.3 5.9 + - - +
69B LEU* 3.0 20.1 + - - +
107B ILE* 3.9 17.7 - - - -
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE 3.0 20.0 + - - +
63B GLN* 3.9 4.7 - - - +
64B THR 3.3 0.2 - - - -
65B GLY* 1.3 75.8 - - - +
67B THR* 1.3 58.1 + - - +
69B LEU* 2.8 6.8 + - + +
70B ASN* 2.6 52.4 + - + +
85B MET* 3.5 33.7 - - + -
89B VAL* 4.1 22.2 - - + -
107B ILE* 4.4 6.0 - - + +
109B LEU* 4.2 14.4 - - + -
182B PRO* 3.5 31.9 - - + -
183B VAL* 3.6 28.5 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLN* 3.1 21.0 + - - +
64B THR* 3.7 6.7 - - - -
66B PHE* 1.3 81.7 - - - +
68B LYS* 1.3 65.2 + - + +
70B ASN* 3.4 7.4 + - - +
71B SER* 3.0 29.6 + - - +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.7 22.5 - - + +
52B SER 5.2 4.8 + - - -
53B VAL* 5.5 2.8 - - - +
64B THR* 3.3 34.3 - - - +
65B GLY* 3.5 6.3 - - - +
66B PHE 3.2 0.4 - - - -
67B THR* 1.3 79.6 - - + +
69B LEU* 1.3 63.3 + - - +
71B SER* 3.0 16.4 + - - -
72B TYR* 3.2 10.9 + - - +
124B GLU* 4.0 27.4 - - - +
126B ASP* 3.0 27.8 + - - +
127B VAL* 4.0 17.3 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.3 39.8 - - + +
50B SER 3.7 6.1 - - - +
51B THR* 3.3 21.3 - - - +
65B GLY 3.0 7.5 + - - +
66B PHE* 2.8 12.2 + - + +
68B LYS* 1.3 74.1 - - - +
70B ASN* 1.3 62.3 + - - +
72B TYR* 3.3 15.5 + - - +
73B ILE* 3.5 16.6 + - - +
107B ILE* 3.3 42.6 - - + +
108B SER* 3.6 15.5 - - - +
109B LEU* 3.7 20.1 - - + +
127B VAL* 4.3 5.8 - - + -
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Residues in contact with ASN 70 (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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66B PHE* 2.6 41.5 + - + +
67B THR* 3.8 7.4 - - - +
69B LEU* 1.3 72.0 - - - +
71B SER* 1.3 64.3 + - - +
73B ILE* 3.3 25.9 - - - +
74B GLN* 3.0 52.3 + - - +
85B MET* 3.7 8.0 - - - +
109B LEU* 4.8 2.4 - - - +
183B VAL* 6.3 0.8 - - - +
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Residues in contact with SER 71 (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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67B THR* 3.0 19.6 + - - +
68B LYS* 3.0 12.3 + - - -
70B ASN* 1.3 77.2 - - - +
72B TYR* 1.3 61.8 + - - +
74B GLN* 3.2 15.1 + - - +
75B GLY 3.3 2.6 + - - +
76B LYS* 3.1 43.9 + - - +
124B GLU* 4.2 7.3 + - - -
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Residues in contact with TYR 72 (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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49B VAL* 3.8 32.1 - - + -
68B LYS 3.2 7.9 + - - +
69B LEU 3.6 8.3 - - - +
70B ASN 3.2 0.6 - - - -
71B SER* 1.3 79.6 - - - +
73B ILE* 1.3 68.9 + - + +
76B LYS* 4.1 11.2 - - - +
77B ASN* 2.9 45.0 + - + -
81B MET 4.4 0.2 - - - +
83B ILE* 3.8 18.8 - - + +
111B ILE* 5.0 4.9 - - + -
119B PRO* 3.8 9.4 - - - +
120B PRO* 2.6 49.9 + - + +
122B PRO* 3.5 33.0 - - + -
127B VAL* 4.6 7.4 - - + -
129B ILE* 3.8 8.3 - - + +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 5.0 4.0 - - + -
69B LEU 3.5 8.0 + - - +
70B ASN* 3.3 35.7 - - - +
72B TYR* 1.3 90.6 - - + +
74B GLN* 1.3 62.0 + - + +
75B GLY 3.1 5.4 - - - -
81B MET 4.5 0.2 - - - -
82B LYS* 3.3 6.9 - - - +
83B ILE* 2.7 67.1 + - + +
84B LYS 5.1 1.6 - - - +
85B MET* 3.7 34.1 - - + -
109B LEU* 4.5 11.7 - - + -
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Residues in contact with GLN 74 (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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70B ASN* 3.0 49.0 + - - +
71B SER* 3.2 8.3 + - - +
73B ILE* 1.3 80.5 - - - +
75B GLY* 1.3 60.4 + - - +
82B LYS* 3.3 41.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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