Contacts of the helix formed by residues 50 - 64 (chain G) in PDB entry 2ZJR
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 PRO 50 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G GLY 3.7 0.6 - - - -
49G VAL* 1.3 91.1 - - + +
51G LEU* 1.3 66.1 + - - +
52G GLY 2.9 5.2 + - - +
53G ARG* 3.0 29.3 + - + +
54G LEU 3.3 8.1 + - - -
89G ALA* 3.3 14.1 - - + +
90G LEU* 6.1 0.4 - - - -
91G THR* 5.8 1.6 - - - +
1150X C 4.8 3.1 - - - +
1151X U 4.6 21.1 - - - +
1152X C 3.3 40.8 - - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G VAL 3.2 3.4 + - - -
50G PRO* 1.3 67.5 - - - +
52G GLY* 1.3 52.7 + - - +
54G LEU* 3.5 6.5 + - + +
55G ALA* 2.7 39.3 + - + +
88G VAL* 3.4 20.4 - - + +
89G ALA 3.1 13.7 + - - +
90G LEU* 4.1 14.6 - - + -
98G LYS* 4.8 5.4 - - - +
116G ARG* 4.6 2.2 - - - +
126G VAL* 3.5 30.3 - - + +
127G ILE* 3.3 45.8 - - + -
130G ALA* 4.4 4.7 - - + -
131G VAL* 6.5 0.7 - - + -
1149X G 4.4 20.6 - - - +
1150X C 4.2 4.4 + - - +
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Residues in contact with GLY 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G PRO 2.9 2.6 + - - -
51G LEU* 1.3 78.2 - - - +
53G ARG* 1.3 64.1 + - - +
55G ALA* 2.8 24.0 + - - +
56G THR* 2.9 9.2 + - - -
134G MET* 4.9 0.6 - - - +
1149X G 3.4 30.0 + - - -
1150X C 3.2 14.0 + - - -
1154X A 3.8 6.9 + - - -
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Residues in contact with ARG 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G VAL* 4.6 10.6 - - + +
50G PRO* 3.0 28.9 + - + +
52G GLY* 1.3 71.4 - - - +
54G LEU* 1.3 63.2 + - - +
56G THR* 3.4 3.6 + - - -
57G LEU* 3.2 21.5 + - - +
170G PRO* 4.1 9.9 - - - +
171G LEU* 3.1 58.1 - - - +
1023X U 3.6 30.4 - - + +
1150X C 5.0 1.6 - - - -
1152X C 4.1 17.6 + - - -
1154X A 4.1 5.7 - - - +
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Residues in contact with LEU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G VAL* 3.4 16.8 - - + -
45G ASP 3.3 22.9 - - - +
46G ALA* 3.3 32.8 - - + +
49G VAL* 3.9 17.4 - - + +
50G PRO 3.3 4.5 + - - +
51G LEU* 3.7 9.0 - - + +
52G GLY 3.2 0.4 - - - -
53G ARG* 1.3 75.9 - - - +
55G ALA* 1.3 71.6 + - - +
57G LEU* 3.3 8.3 + - + +
58G ILE* 2.9 46.8 + - + +
82G VAL* 5.0 2.7 - - + -
88G VAL* 5.3 4.9 - - + -
127G ILE* 5.3 8.1 - - + -
170G PRO* 3.4 18.8 - - + -
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 2.7 20.5 + - + +
52G GLY* 2.8 17.9 + - - +
54G LEU* 1.3 74.6 - - - +
56G THR* 1.3 54.0 + - - +
58G ILE* 2.7 28.7 + - - +
59G ALA 2.7 10.7 + - - -
130G ALA* 4.3 4.7 - - + +
131G VAL* 4.0 16.6 - - + -
134G MET* 3.0 27.6 - - + -
1149X G 5.5 2.5 - - - -
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Residues in contact with THR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G GLY 2.9 10.0 + - - -
53G ARG 3.7 2.9 - - - -
55G ALA* 1.3 75.3 - - - +
57G LEU* 1.3 52.2 + - - +
59G ALA* 3.6 1.9 - - - +
60G SER* 2.5 42.8 + - - +
134G MET* 3.4 7.7 - - - +
1016X C 2.8 45.4 + - - +
1017X C 3.3 28.9 + - - +
1023X U 3.6 13.2 - - + +
1148X G 3.8 8.5 + - - -
1154X A 3.8 3.6 + - - -
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G VAL* 4.4 22.7 - - + -
53G ARG* 3.2 11.0 + - - +
54G LEU* 3.4 9.6 - - + +
55G ALA 2.7 3.8 + - - -
56G THR* 1.3 74.8 - - - +
58G ILE* 1.3 70.0 + - + +
60G SER* 3.0 5.5 + - - -
61G ARG* 3.0 35.8 + - + +
65G LYS* 3.7 26.5 - - - +
168G THR 4.6 2.5 - - - +
169G GLN 4.5 2.9 - - - +
170G PRO* 3.7 38.8 - - + +
171G LEU* 5.6 5.8 - - + -
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Residues in contact with ILE 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G VAL* 4.2 13.9 - - + -
54G LEU* 2.9 40.4 + - + +
55G ALA* 2.7 11.9 + - - +
57G LEU* 1.3 77.9 - - + +
59G ALA* 1.3 63.2 + - - +
61G ARG* 3.4 2.2 + - - +
62G ILE* 3.0 44.6 + - + +
80G VAL* 3.8 25.5 - - + +
82G VAL* 3.3 28.0 - - + -
127G ILE* 4.9 9.9 - - + -
131G VAL* 4.3 13.0 - - + -
148G LEU* 4.6 8.3 - - + -
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ALA 2.7 17.9 + - - +
56G THR* 3.6 5.2 - - - +
58G ILE* 1.3 74.3 - - - +
60G SER* 1.3 61.3 + - - +
62G ILE* 3.3 2.1 + - - -
63G ARG* 3.1 20.3 + - - +
131G VAL* 4.2 9.8 - - + +
134G MET* 3.7 37.9 - - + +
135G LEU* 3.3 19.5 - - + +
1017X C 4.0 9.6 - - - +
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G THR* 2.5 29.9 + - - +
57G LEU* 3.0 7.8 + - - -
59G ALA* 1.3 69.7 - - - +
61G ARG* 1.3 55.5 + - - +
62G ILE 3.0 5.6 + - - -
63G ARG* 3.2 5.3 + - - +
64G GLY 2.8 39.3 + - - +
65G LYS* 4.1 8.7 - - - -
1017X C 3.2 29.8 - - - -
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Residues in contact with ARG 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ASN* 4.7 5.1 - - - +
42G VAL* 4.1 21.2 - - - +
44G VAL* 5.8 3.1 - - - -
57G LEU* 3.0 27.3 + - + +
58G ILE* 4.2 3.6 - - - +
60G SER* 1.3 73.8 - - - +
62G ILE* 1.3 59.0 + - - +
64G GLY 4.0 1.5 + - - -
65G LYS* 2.5 63.8 + - + +
66G HIS* 4.7 4.9 - - - +
77G GLY* 3.1 24.1 - - - -
78G ASP* 2.4 55.4 + - - +
80G VAL* 4.3 10.9 - - + +
168G THR* 4.2 20.1 + - - +
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G ILE* 3.0 40.6 - - + +
59G ALA* 3.4 9.0 - - - +
60G SER 3.0 0.2 - - - -
61G ARG* 1.3 78.1 - - - +
63G ARG* 1.3 61.9 + - - +
75G ILE* 4.8 3.1 - - - +
77G GLY* 2.9 28.4 + - - +
78G ASP 4.3 2.2 - - - +
80G VAL* 3.5 17.9 - - + -
131G VAL* 4.5 2.2 - - + -
135G LEU* 3.9 28.5 - - + -
144G MET* 3.9 26.3 - - + +
147G ARG* 4.8 9.2 + - + -
148G LEU* 3.7 28.7 - - + +
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Residues in contact with ARG 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ALA 3.1 12.6 + - - +
60G SER* 3.9 4.9 - - - +
62G ILE* 1.3 80.6 - - - +
64G GLY* 1.3 60.1 + - - +
67G ARG* 4.3 18.6 - - - +
71G THR 3.8 9.3 + - - -
72G PRO* 3.4 26.2 + - - +
74G MET 3.9 5.7 + - - -
75G ILE* 4.1 7.0 - - - +
76G GLN 4.9 1.4 + - - -
77G GLY* 4.3 5.6 + - - -
135G LEU* 4.4 8.7 - - + -
136G PRO* 4.0 27.2 - - + +
140G GLN* 2.9 32.5 - - - +
144G MET* 3.7 13.9 - - - +
567X G 5.7 3.8 + - - -
1017X C 5.7 1.3 - - - +
1018X C 4.2 20.6 - - - +
1019X U 5.2 6.8 + - - -
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Residues in contact with GLY 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G SER* 2.8 9.6 + - - +
62G ILE 3.2 2.2 - - - -
63G ARG* 1.3 82.0 - - - +
65G LYS* 1.3 70.0 + - - +
67G ARG* 3.2 31.4 - - - -
68G PRO* 5.8 0.4 - - - -
77G GLY* 4.2 12.8 - - - -
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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