Contacts of the helix formed by residues 63 - 76 (chain O) in PDB entry 5GSE
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 ARG 63 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163I A 3.3 43.6 + - - +
164I A 3.9 20.7 + - - +
91J A 3.8 16.4 - - - +
92J C 3.4 20.4 - - - +
60O LEU 4.3 15.6 + - - -
61O LEU* 4.4 10.1 + - - +
62O ILE* 1.3 76.6 + - - +
64O LYS* 1.3 66.1 + - - +
65O LEU 3.5 0.2 - - - -
66O PRO* 3.3 29.5 - - + +
67O PHE* 3.4 12.1 + - - +
30P THR* 5.2 7.0 - - + +
33P ALA* 4.9 2.2 - - - +
36P ARG* 3.7 25.4 - - - +
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Residues in contact with LYS 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J C 3.0 42.8 + - - +
93J C 4.1 21.2 + - - +
60O LEU* 6.6 0.2 - - + -
62O ILE 3.6 3.0 + - - -
63O ARG* 1.3 71.8 - - - +
65O LEU* 1.3 80.2 + - + +
67O PHE* 3.2 5.2 + - - +
68O GLN* 2.9 33.8 + - + +
89O VAL* 6.6 0.2 - - + -
90O MET* 5.7 8.7 - - - -
93O GLN* 4.4 14.2 - - - +
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Residues in contact with LEU 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J A 4.1 28.0 - - + +
92J C 3.1 32.5 + - + +
93J C 6.0 0.2 - - - +
64O LYS* 1.3 102.8 - - + +
66O PRO* 1.3 71.2 - - + +
68O GLN* 3.2 24.7 + - - +
69O ARG* 3.0 32.9 + - + +
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Residues in contact with PRO 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J A 3.8 22.0 - - - +
63O ARG* 3.3 34.8 - - + +
65O LEU* 1.3 92.7 - - + +
67O PHE* 1.3 55.7 + - - +
69O ARG* 3.3 20.0 + - - +
70O LEU* 2.9 28.6 + - - +
25P ASN* 5.0 3.5 - - - +
28P GLY* 3.5 30.3 - - - +
29P ILE* 4.8 3.5 - - + +
30P THR* 6.1 1.6 - - + -
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Residues in contact with PHE 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62O ILE* 3.3 31.6 - - + -
63O ARG 3.4 7.6 + - - +
64O LYS 3.2 8.9 + - - +
66O PRO* 1.3 77.4 - - - +
68O GLN* 1.3 60.9 + - - +
70O LEU* 3.2 9.8 + - + +
71O VAL* 2.9 51.1 + - + +
89O VAL* 3.8 11.0 - - + -
92O LEU* 3.7 11.2 - - + -
93O GLN* 3.3 52.9 - - + +
96O CYS* 3.7 21.1 - - + -
29P ILE* 4.4 10.2 - - + +
58P LEU* 5.1 2.9 - - + -
62P LEU* 3.7 18.6 - - + -
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Residues in contact with GLN 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I T 5.5 0.4 + - - -
64O LYS* 2.9 21.5 + - + +
65O LEU* 3.2 28.3 + - + +
67O PHE* 1.3 81.7 - - - +
69O ARG* 1.3 61.9 + - + +
71O VAL* 3.3 7.4 + - - +
72O ARG* 3.0 64.7 + - - +
89O VAL* 4.6 22.4 - - + +
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Residues in contact with ARG 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J A 3.0 40.4 + - - -
65O LEU* 3.0 19.3 + - - +
66O PRO* 3.9 22.2 + - - +
68O GLN* 1.3 79.0 - - + +
70O LEU* 1.3 65.2 + - - +
72O ARG* 3.3 4.9 + - - +
73O GLU* 2.9 23.2 + - - +
22P LEU* 3.5 40.3 - - + +
25P ASN* 2.9 30.8 + - - +
28P GLY* 6.0 2.2 - - - -
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Residues in contact with LEU 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O PRO 2.9 14.3 + - - +
67O PHE* 3.4 11.9 - - + +
69O ARG* 1.3 77.4 - - - +
71O VAL* 1.3 62.7 + - - +
73O GLU* 3.2 6.0 + - - +
74O ILE* 2.9 51.9 + - + +
25P ASN* 4.0 32.4 - - + +
26P ILE* 4.1 18.8 - - + +
29P ILE* 3.6 32.1 - - + -
58P LEU* 4.4 7.2 - - + -
59P LYS* 4.8 2.5 - - + -
62P LEU* 4.0 19.3 - - + -
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Residues in contact with VAL 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O PHE* 2.9 51.0 + - + +
68O GLN* 3.3 9.2 + - - +
70O LEU* 1.3 74.9 - - - +
72O ARG* 1.3 58.0 + - + +
74O ILE* 4.6 1.1 - - - -
75O ALA* 2.9 28.1 + - - +
84O PHE* 3.6 33.4 - - + -
89O VAL* 4.8 9.2 - - + -
92O LEU* 3.8 13.9 - - + -
62P LEU* 4.0 11.7 - - + -
66P ILE* 3.7 16.5 - - + +
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Residues in contact with ARG 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I T 2.7 42.3 + - - -
155I G 5.3 10.4 + - - -
68O GLN* 3.0 57.1 + - - +
69O ARG* 3.7 9.4 - - - +
70O LEU 3.2 0.2 - - - -
71O VAL* 1.3 78.9 - - - +
73O GLU* 1.3 61.4 + - - +
75O ALA* 3.2 6.5 + - - +
76O GLN* 3.0 33.7 + - + +
82O LEU 5.0 5.7 + - - +
83O ARG* 5.0 0.6 - - - +
84O PHE* 4.2 22.4 + - + +
89O VAL* 4.8 10.5 - - - +
22P LEU* 4.0 17.3 - - + -
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Residues in contact with GLU 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O ARG 2.9 16.5 + - - +
70O LEU* 3.8 8.0 - - - +
72O ARG* 1.3 77.0 - - - +
74O ILE* 1.3 66.0 + - + +
76O GLN* 3.3 25.1 + - - +
77O ASP* 4.1 8.1 + - - +
22P LEU* 3.5 19.4 - - + +
23P ARG* 3.2 14.8 - - + +
24P ASP* 3.3 12.6 + - - -
25P ASN* 2.4 50.1 + - - +
26P ILE* 4.9 1.6 + - - +
59P LYS* 5.5 5.7 + - - +
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Residues in contact with ILE 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O LEU* 2.9 47.8 + - + +
71O VAL 3.9 2.9 - - - +
73O GLU* 1.3 79.5 - - + +
75O ALA* 1.3 63.6 + - - +
76O GLN 3.3 0.5 + - - -
77O ASP* 3.3 25.3 + - - +
78O PHE* 4.0 8.2 - - + -
59P LYS* 3.9 30.5 - - + +
62P LEU* 3.9 26.5 - - + -
63P GLU* 3.7 33.4 - - + -
66P ILE* 3.9 14.4 - - + -
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Residues in contact with ALA 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O VAL 2.9 19.3 + - - +
72O ARG 3.2 3.6 + - - +
74O ILE* 1.3 77.3 - - - +
76O GLN* 1.3 62.6 + - - +
77O ASP 3.1 1.2 + - - -
78O PHE* 3.2 12.5 + - - +
79O LYS 2.8 16.6 + - - +
82O LEU* 4.2 11.2 - - + +
84O PHE* 3.3 33.4 - - + -
66P ILE* 3.9 18.6 - - + +
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Residues in contact with GLN 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J C 5.5 1.7 - - - +
72O ARG* 3.0 23.5 + - + +
73O GLU* 3.6 13.7 - - - +
74O ILE 3.2 1.0 - - - -
75O ALA* 1.3 76.1 - - - +
77O ASP* 1.3 62.9 + - - +
79O LYS 3.3 18.1 - - - +
80O THR* 3.8 40.0 + - + +
21P VAL* 3.2 30.7 - - - +
22P LEU* 3.9 23.2 + - - +
23P ARG* 4.6 6.8 + - - -
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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