Contacts of the helix formed by residues 59 - 75 (chain B) in PDB entry 3G2U
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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11A GLU* 3.8 31.8 - - + +
14A ILE* 4.4 2.0 - - - +
15A ASN* 2.9 42.6 + - - -
50A LEU* 4.3 6.6 - - + +
54A LYS* 4.3 1.6 - - - +
148A IOD 3.2 26.2 - - + +
20B PRO* 3.7 14.8 - - + +
57B SER* 2.8 12.1 + - - +
58B PRO* 1.3 78.0 - - - +
60B GLU* 1.3 66.0 + - - +
61B TRP 3.2 2.5 - - - -
62B GLU* 2.9 35.6 + - + +
63B ALA 3.2 4.2 + - - -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 5.0 1.1 - - - -
58B PRO 3.5 6.2 + - - +
59B GLN* 1.3 70.9 - - - +
61B TRP* 1.3 57.3 + - - +
63B ALA* 3.0 10.6 + - - +
64B ILE* 2.8 38.9 + - + +
108B SER* 2.6 32.6 + - - +
110B LYS* 3.7 18.4 - - - +
111B VAL* 3.9 9.6 - - + -
148B IOD 3.4 19.8 - - + +
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Residues in contact with TRP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 3.5 26.9 - - + -
22B ASN* 2.8 28.5 + - - +
23B LYS 4.7 2.5 - - - -
24B GLU* 4.2 15.5 - - - -
25B LEU* 4.0 23.3 - - + -
59B GLN* 3.2 1.0 - - + -
60B GLU* 1.3 75.0 - - - +
62B GLU* 1.3 64.6 + - - +
64B ILE* 4.0 18.6 - - + -
65B GLN* 3.1 61.6 + - + +
110B LYS* 5.7 0.9 - - - -
148B IOD 3.8 27.5 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 5.7 0.2 - - - +
53A HIS* 4.2 8.6 + - - -
54A LYS* 4.9 10.4 + - - -
18B THR* 3.7 25.7 + - - +
20B PRO* 4.2 23.8 - - + +
54B LYS* 4.2 32.7 + - + +
57B SER* 2.5 33.6 + - - +
59B GLN* 2.9 26.3 + - + +
61B TRP* 1.3 79.3 - - - +
63B ALA* 1.3 60.7 + - - +
65B GLN* 3.7 0.4 + - - +
66B ALA* 3.2 22.5 + - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS 3.5 12.6 - - - +
55B ILE* 3.5 25.3 - - - +
57B SER* 4.0 15.0 - - - +
59B GLN 3.2 1.7 + - - +
60B GLU* 3.0 9.3 + - - +
62B GLU* 1.3 76.2 - - - +
64B ILE* 1.3 60.3 + - - +
66B ALA* 3.4 2.1 + - - +
67B LEU* 3.0 35.8 + - - +
111B VAL* 4.2 17.9 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 5.9 0.9 - - + -
60B GLU* 2.8 32.5 + - + +
61B TRP* 4.0 26.2 - - + +
63B ALA* 1.3 72.9 - - - +
65B GLN* 1.3 65.6 + - - +
67B LEU* 3.1 11.2 + - + +
68B THR* 3.0 29.5 + - - +
110B LYS* 3.8 34.8 - - + +
111B VAL* 3.6 27.1 - - + -
114B LYS* 5.0 7.6 - - + +
148B IOD 4.0 7.0 - - + -
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA 3.3 17.2 - - - +
18B THR* 3.3 19.1 + - - -
19B ASN 3.1 22.2 + - - -
22B ASN* 2.9 30.1 + - - +
24B GLU 4.5 2.4 - - - +
25B LEU* 4.1 12.7 - - + -
30B ILE* 5.1 1.8 - - + +
61B TRP* 3.1 58.6 + - + +
62B GLU 3.9 0.7 - - - +
64B ILE* 1.3 77.3 - - - +
66B ALA* 1.3 57.2 + - - +
68B THR* 3.3 10.6 - - - -
69B VAL* 2.9 29.6 + - - +
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Residues in contact with ALA 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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18B THR* 3.7 14.2 - - + +
51B LEU* 3.6 9.7 - - + +
54B LYS* 3.6 27.8 - - + -
55B ILE* 4.0 13.6 - - + +
62B GLU 3.2 15.3 + - - +
63B ALA 3.7 5.4 - - - +
64B ILE 3.3 0.2 - - - -
65B GLN* 1.3 76.9 - - - +
67B LEU* 1.3 60.0 + - - +
69B VAL* 3.2 6.4 + - - +
70B LEU* 2.9 27.2 + - - +
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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
----------------------------------------------------------
55B ILE* 3.8 28.3 - - + -
63B ALA 3.0 23.3 + - - +
64B ILE* 3.7 7.4 - - + +
66B ALA* 1.3 74.0 - - - +
68B THR* 1.3 58.1 + - - +
70B LEU* 3.7 10.0 - - + +
71B GLU* 2.9 28.9 + - - +
94B LEU* 4.4 1.8 - - + -
111B VAL* 3.9 37.0 - - + +
114B LYS* 4.1 24.9 - - + -
115B ILE* 3.6 24.2 - - + -
118B LEU* 3.7 21.3 - - + +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.2 24.3 - - + +
27B TRP* 4.0 25.6 - - + -
30B ILE* 4.5 6.1 - - + -
64B ILE* 3.0 19.2 + - - +
65B GLN* 3.3 13.2 - - - -
67B LEU* 1.3 74.5 - - - +
69B VAL* 1.3 59.8 + - - +
71B GLU* 3.7 14.4 + - - +
72B THR* 2.6 36.4 + - - +
114B LYS* 5.3 4.9 - - - +
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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
----------------------------------------------------------
14B ILE* 4.0 10.3 - - + -
17B ALA* 4.0 27.1 - - + +
18B THR* 4.1 4.5 - - + -
30B ILE* 4.1 20.4 - - + +
33B PHE* 3.5 34.8 - - + -
34B CYS* 4.6 2.2 - - - -
51B LEU* 3.7 15.0 - - + -
65B GLN 2.9 20.5 + - - +
66B ALA 3.2 6.7 + - - +
68B THR* 1.3 74.6 - - - +
70B LEU* 1.3 65.1 + - - +
72B THR* 3.3 3.1 + - - -
73B CYS* 3.0 27.3 + - - -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.0 15.4 - - + +
55B ILE* 3.8 22.2 - - + -
66B ALA 2.9 16.1 + - - +
67B LEU* 3.7 16.8 - - + +
69B VAL* 1.3 77.7 - - - +
71B GLU* 1.3 62.4 + - - +
73B CYS* 3.4 2.7 + - - +
74B MET* 3.0 32.4 + - + +
81B PHE* 4.0 9.6 - - + -
85B VAL* 3.9 27.6 - - + -
90B PHE* 3.9 20.2 - - + -
94B LEU* 4.5 4.7 - - + -
118B LEU* 4.4 2.5 - - + -
122B TRP* 3.6 25.4 - - + -
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Residues in contact with GLU 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 LEU 2.9 20.8 + - - +
68B THR* 3.7 14.9 + - - +
69B VAL 3.3 0.2 - - - -
70B LEU* 1.3 73.4 - - - +
72B THR* 1.3 64.2 + - - +
74B MET* 3.6 6.1 + - - +
75B LYS* 3.2 51.8 + - + +
114B LYS* 2.8 33.5 + - - -
117B GLU* 4.6 2.1 - - - +
118B LEU* 3.6 23.8 - - + +
122B TRP* 5.0 1.2 + - - +
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Residues in contact with THR 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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27B TRP* 3.6 23.9 - - + -
30B ILE* 3.9 9.3 - - + +
31B ASN* 3.5 28.5 - - - +
34B CYS* 4.1 9.1 - - + +
68B THR* 2.6 23.4 + - - +
69B VAL 3.6 3.8 - - - -
70B LEU 3.3 0.2 - - - -
71B GLU* 1.3 78.9 - - - +
73B CYS* 1.3 60.5 + - - +
75B LYS* 3.2 20.6 + - - +
76B SER* 3.5 9.0 + - - -
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Residues in contact with CYS 73 (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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33B PHE* 3.8 13.2 - - - -
34B CYS* 2.0 57.0 - - + +
37B LEU* 3.8 14.1 - - + -
69B VAL* 3.0 21.2 + - - +
70B LEU 4.1 0.7 - - - +
72B THR* 1.3 72.5 - - - +
74B MET* 1.3 66.3 + - - +
75B LYS 3.1 1.6 - - - -
76B SER* 3.3 19.9 + - - +
81B PHE* 3.5 31.4 - - + +
82B HIS* 4.6 0.7 + - - -
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Residues in contact with MET 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 LEU* 3.0 25.1 + - + +
71B GLU 3.8 3.8 - - - +
73B CYS* 1.3 78.9 - - - +
75B LYS* 1.3 59.3 + - + +
81B PHE* 3.6 19.7 - - + -
82B HIS* 2.7 47.9 + - + +
85B VAL* 3.7 29.8 - - + -
122B TRP* 3.6 42.8 - - + +
126B LEU* 3.5 33.9 - - + +
132B ILE* 4.6 4.0 - - + -
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Residues in contact with LYS 75 (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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71B GLU* 3.2 43.2 + - + +
72B THR* 3.5 13.2 - - + +
73B CYS 3.1 1.4 - - - -
74B MET* 1.3 78.0 - - + +
76B SER* 1.3 59.9 + - - +
82B HIS* 5.6 0.2 - - - -
122B TRP* 6.4 0.2 - - - +
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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