Contacts of the helix formed by residues 64 - 81 (chain P) in PDB entry 2ZJQ
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 ALA 64 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 4.0 5.8 - - - -
37P LYS* 3.1 28.8 - - + +
38P VAL* 3.9 20.5 - - + +
41P VAL* 3.3 26.2 - - + -
62P ARG* 2.9 1.5 - - + -
63P SER* 1.3 77.6 - - - +
65P SER* 1.3 60.3 + - - +
67P PRO* 3.9 4.6 - - - +
68P VAL* 2.8 31.3 + - - +
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Residues in contact with SER 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P VAL* 4.1 3.9 - - - +
57P LEU* 4.0 29.3 - - - +
60P ILE* 3.1 37.3 + - - +
62P ARG 3.0 19.3 + - - -
63P SER 3.0 1.8 - - - -
64P ALA* 1.3 76.6 - - - +
66P GLU* 1.3 71.1 + - - +
68P VAL* 3.2 4.2 + - - +
69P ALA* 3.0 16.9 + - - +
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Residues in contact with GLU 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K ARG* 4.8 11.8 + - - -
63P SER* 4.1 5.0 + - - +
65P SER* 1.3 73.9 - - - +
67P PRO* 1.3 64.6 - - + +
69P ALA* 2.4 43.1 + - + +
70P LYS* 3.1 32.5 + - + -
1297X A 4.7 15.5 + - - +
1298X G 5.0 9.7 + - - +
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Residues in contact with PRO 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P VAL* 4.1 20.2 - - + -
33P MET* 4.3 13.5 - - + -
63P SER 3.8 13.9 - - - +
64P ALA 3.9 3.6 - - - +
65P SER 3.9 1.1 - - - -
66P GLU* 1.3 92.5 - - + +
68P VAL* 1.3 55.8 + - - +
69P ALA 2.3 14.7 + - - -
70P LYS* 2.8 22.0 + - + +
71P VAL* 3.1 16.0 + - + +
124P ILE* 4.0 18.8 - - + -
501X G 6.0 0.9 - - - +
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Residues in contact with VAL 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P VAL* 3.8 25.8 - - + -
41P VAL* 4.2 6.7 - - + -
42P VAL* 3.8 27.1 - - + -
45P ILE* 4.4 22.7 - - + -
57P LEU* 3.6 9.8 - - + +
64P ALA 2.8 26.9 - - - +
65P SER 3.2 4.8 + - - +
66P GLU 3.2 0.2 + - - -
67P PRO* 1.3 74.1 - - - +
69P ALA* 1.3 60.9 + - - +
71P VAL* 4.1 6.4 - - + +
72P LEU* 3.5 16.3 + - - +
124P ILE* 4.2 13.0 - - + +
126P ILE* 5.4 3.5 - - + +
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Residues in contact with ALA 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU* 3.3 19.7 - - + -
65P SER 3.0 8.2 + - - +
66P GLU* 2.4 29.5 + - + +
67P PRO 2.3 11.1 + - - -
68P VAL* 1.3 63.7 - - - +
70P LYS* 1.3 52.4 + - + +
71P VAL 2.4 4.2 + - - -
72P LEU* 2.2 34.9 + - - +
73P ASN* 3.0 10.7 + - - -
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Residues in contact with LYS 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P GLU* 3.1 33.3 + - + +
67P PRO* 2.8 15.8 + - + +
69P ALA* 1.3 75.8 - - + +
71P VAL* 1.3 61.6 + - + +
73P ASN* 4.0 9.8 + - - +
74P SER* 3.6 17.0 - - - -
498X C 4.7 4.3 + - - +
499X G 3.1 40.3 + - - +
500X G 2.8 45.8 + - - -
501X G 3.2 23.1 + - - +
502X A 5.2 6.4 + - - +
503X G 5.2 2.3 + - - -
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Residues in contact with VAL 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ALA* 3.8 17.7 - - + +
27P VAL 4.1 1.1 - - - +
28P ALA* 3.3 31.9 - - + +
67P PRO* 3.5 17.9 - - + +
68P VAL* 4.4 3.8 - - - +
69P ALA 2.4 10.1 + - - -
70P LYS* 1.3 71.4 - - + +
72P LEU* 1.3 64.1 + - - +
74P SER* 3.2 5.0 + - - -
75P ALA* 3.0 18.9 + - - +
124P ILE* 3.6 27.8 - - + +
126P ILE* 3.1 27.8 - - + +
503X G 6.1 0.9 - - - +
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Residues in contact with LEU 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P ILE* 4.9 5.6 - - + -
50P VAL* 4.3 12.8 - - + -
53P ALA* 3.3 34.1 - - + +
54P GLU* 4.2 15.0 - - + +
57P LEU* 4.9 6.3 - - + -
68P VAL 3.5 12.8 + - - +
69P ALA* 2.2 25.3 + - - +
71P VAL* 1.3 68.2 - - - +
73P ASN* 1.3 56.3 + - - +
74P SER 2.7 11.7 + - - -
75P ALA 3.3 0.9 + - - +
76P LYS* 3.3 20.4 + - - +
92P VAL* 3.8 16.4 - - + -
126P ILE* 3.4 30.3 - - + +
128P VAL* 4.3 9.9 - - + -
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Residues in contact with ASN 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P GLU* 3.6 21.8 - - + +
69P ALA 3.0 10.7 + - - +
70P LYS* 4.0 6.5 + - - +
71P VAL 3.3 0.2 - - - -
72P LEU* 1.3 75.0 - - - +
74P SER* 1.3 53.0 + - - +
76P LYS* 3.6 18.6 + - - +
77P ALA* 3.9 8.9 - - - +
498X C 2.3 59.5 + - - +
499X G 4.3 7.7 + - - -
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Residues in contact with SER 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ALA* 3.9 7.5 - - - +
70P LYS 3.6 10.1 - - - -
71P VAL* 3.6 9.2 - - - -
72P LEU 2.7 1.0 + - - -
73P ASN* 1.3 78.7 - - - +
75P ALA* 1.3 65.4 + - - +
76P LYS 2.7 5.5 + - - +
77P ALA* 3.5 6.5 - - - +
78P ASN* 3.0 37.2 + - - -
498X C 2.4 35.1 + - - -
503X G 3.6 9.2 + - - -
504X G 4.4 3.1 + - - -
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Residues in contact with ALA 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLY* 3.9 4.0 - - - -
25P PHE 4.1 5.4 - - - -
26P ALA* 3.3 16.5 - - + +
71P VAL 3.0 12.4 + - - +
72P LEU 3.9 4.7 - - - +
74P SER* 1.3 75.6 - - - +
76P LYS* 1.3 53.5 + - - +
78P ASN* 4.3 0.4 - - - +
79P ALA* 3.4 10.0 + - - +
126P ILE* 3.2 34.1 - - + +
128P VAL* 2.6 44.5 - - + +
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Residues in contact with LYS 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P VAL* 5.2 22.0 - - + +
54P GLU* 3.0 34.0 + - + +
72P LEU 3.3 14.9 + - - +
73P ASN* 3.6 19.1 + - - +
74P SER 2.7 1.8 - - - +
75P ALA* 1.3 77.9 - - - +
77P ALA* 1.3 56.3 + - - +
78P ASN 2.5 5.7 + - - -
79P ALA* 2.5 31.4 + - - +
80P LEU* 2.9 24.0 + - + +
87P GLU* 4.0 30.2 + - - -
90P LEU* 4.5 10.1 - - + -
128P VAL* 4.4 2.2 - - + -
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Residues in contact with ALA 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P ASN* 3.9 3.8 - - - +
74P SER* 3.5 8.4 - - - +
76P LYS* 1.3 81.0 - - - +
78P ASN* 1.3 62.5 + - - +
80P LEU* 4.0 7.6 - - - +
81P HIS* 3.3 27.1 + - - +
497X C 3.8 11.5 + - - +
498X C 2.9 43.5 - - - +
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Residues in contact with ASN 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P PHE 3.4 20.1 - - - +
26P ALA* 4.6 0.7 - - - +
74P SER* 3.0 20.9 + - - +
75P ALA 4.3 2.0 - - - +
76P LYS 2.5 5.1 + - - -
77P ALA* 1.3 76.5 - - - +
79P ALA* 1.3 63.2 + - - +
80P LEU 2.8 6.3 + - - -
82P ASN* 3.5 10.5 + - - +
83P ASP* 3.1 29.2 + - - +
497X C 3.4 11.5 + - - -
498X C 5.5 0.2 + - - -
504X G 3.0 29.0 + - - +
505X G 2.8 39.0 - - - +
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Residues in contact with ALA 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLY* 4.4 1.1 - - - -
75P ALA 3.4 15.9 + - - +
76P LYS 2.5 16.2 + - - +
78P ASN* 1.3 74.7 - - - +
80P LEU* 1.3 55.9 + - - -
83P ASP* 3.3 8.6 + - - +
85P MET* 2.6 55.6 + - - +
90P LEU* 3.5 17.7 - - + -
128P VAL* 3.4 14.1 - - + -
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Residues in contact with LEU 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P LYS* 2.9 24.8 + - + +
77P ALA* 4.4 6.3 - - - +
78P ASN 2.8 1.6 - - - -
79P ALA* 1.3 84.7 - - - +
81P HIS* 1.3 73.6 + - - +
83P ASP 3.0 0.5 + - - -
84P GLU* 2.4 25.6 + - - -
85P MET 3.9 13.5 - - - +
87P GLU* 3.1 61.7 - - + +
90P LEU* 3.8 6.7 - - + -
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Residues in contact with HIS 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P ALA 3.3 18.1 + - - +
80P LEU* 1.3 85.2 - - - +
82P ASN* 1.3 86.8 + - - +
83P ASP 2.8 7.8 + - - -
84P GLU* 3.1 11.6 + - - +
496X C 2.9 37.2 + - - -
497X C 2.9 33.9 + - - +
505X G 4.1 1.1 - - - -
506X G 5.7 0.6 + - - -
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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