Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 2ZPB
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 SER 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU 6.0 0.4 - - - -
49A GLU 4.7 6.7 - - - -
50A ASP 3.2 11.6 + - - -
51A PHE* 1.3 76.3 - - - +
53A PRO* 1.3 73.9 - - - +
54A ARG* 3.1 30.7 + - - +
55A ARG* 3.1 18.6 + - - +
118A PRO 3.4 5.3 + - - -
119A ILE 3.1 11.8 - - - +
121A GLY 3.8 7.2 - - - +
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Residues in contact with PRO 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE 4.8 0.4 - - - +
52A SER* 1.3 84.6 - - - +
54A ARG* 1.3 70.5 + - - +
55A ARG 3.1 0.7 - - - -
56A GLY 3.3 1.3 + - - -
57A ALA* 2.9 27.9 + - - +
119A ILE 3.4 11.4 - - - +
120A LEU 3.4 22.4 - - - +
121A GLY* 4.1 3.6 - - - +
192A LYS* 3.8 42.4 - - + +
195A LEU* 3.5 8.5 - - + +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER* 3.1 18.9 + - - +
53A PRO* 1.3 93.5 + - - +
55A ARG* 1.3 57.7 + - + +
57A ALA* 3.5 17.4 + - - +
58A GLU* 3.0 27.3 + - - +
187A GLN* 2.7 39.4 + - - +
188A GLU* 4.0 9.6 + - - +
190A VAL 3.0 20.0 + - - -
191A THR* 4.2 9.3 - - - +
192A LYS 4.8 0.4 - - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 3.2 39.9 + - - +
51A PHE* 4.2 5.5 - - - -
52A SER* 3.1 11.6 + - - +
53A PRO 3.1 0.4 - - - -
54A ARG* 1.3 76.0 - - + +
56A GLY* 1.3 65.4 + - - +
58A GLU* 3.1 8.7 + - - +
59A LEU* 3.1 26.7 + - - +
85A GLY 4.6 5.5 + - - -
86A TYR* 3.4 62.8 + - + +
87A LEU 5.4 0.8 + - - -
118A PRO* 3.0 42.7 + - - +
119A ILE* 4.1 4.5 - - - -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO 3.3 1.7 + - - -
55A ARG* 1.3 74.6 - - - +
57A ALA* 1.3 57.2 + - - +
59A LEU* 3.2 15.5 + - - +
60A VAL* 2.9 32.1 + - - +
119A ILE* 3.0 27.9 + - - +
120A LEU* 5.3 0.4 - - - -
169A MET* 4.4 3.5 - - - +
195A LEU* 3.8 17.4 - - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO 2.9 15.6 + - - +
54A ARG* 3.5 24.2 - - - +
56A GLY* 1.3 75.4 - - - +
58A GLU* 1.3 54.9 + - - +
60A VAL* 3.3 2.1 + - - +
61A ALA* 3.0 30.3 + - - +
187A GLN* 3.6 13.4 - - + +
190A VAL* 3.4 38.3 - - + +
195A LEU* 4.0 1.6 - - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG 3.0 12.3 + - - +
55A ARG* 3.1 10.1 + - - +
57A ALA* 1.3 75.8 - - - +
59A LEU* 1.3 62.5 + - - +
61A ALA* 3.5 2.3 + - - +
62A ARG* 3.0 25.2 + - - +
84A TYR* 3.4 29.6 - - + +
86A TYR* 2.6 33.3 + - + -
183A GLN* 4.7 2.7 - - - +
187A GLN* 3.7 29.3 + - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG 3.1 18.5 + - - +
56A GLY* 3.4 8.3 - - - +
58A GLU* 1.3 76.4 - - - +
60A VAL* 1.3 57.1 + - - +
62A ARG* 3.4 5.5 + - - +
63A ALA* 3.0 28.8 + - - +
69A PHE* 3.9 20.0 - - + -
73A LEU* 4.2 5.7 - - + +
80A ALA 4.8 0.2 - - - -
81A VAL* 3.8 34.8 - - + -
84A TYR* 3.6 35.9 - - + -
86A TYR* 4.7 4.3 - - + -
119A ILE* 3.9 19.7 - - + -
169A MET* 4.1 22.2 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 2.9 19.5 + - - +
57A ALA 3.7 4.5 - - - +
59A LEU* 1.3 75.9 - - - +
61A ALA* 1.3 58.3 + - - +
63A ALA* 3.1 3.1 + - - +
64A TRP* 2.9 61.7 + - + -
169A MET* 3.7 21.1 - - + -
171A LEU* 3.8 19.5 - - + -
172A PRO* 4.0 12.8 - - + -
190A VAL* 3.8 16.8 - - + -
195A LEU* 3.7 15.0 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.0 16.8 + - - +
58A GLU 3.9 2.2 - - - +
60A VAL* 1.3 76.6 - - - +
62A ARG* 1.3 59.0 + - - +
64A TRP* 3.4 13.5 + - - +
65A THR* 3.0 31.2 + - - +
183A GLN* 3.6 31.5 - - + +
186A LEU* 3.9 8.0 - - + +
187A GLN* 3.6 18.6 - - + +
190A VAL* 5.1 0.2 - - - +
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU 3.0 15.6 + - - +
59A LEU 3.6 4.5 - - - +
61A ALA* 1.3 72.9 - - - +
63A ALA* 1.3 60.9 + - - +
65A THR* 3.1 4.3 + - - -
66A ASP* 2.9 63.5 + - - +
69A PHE* 3.3 35.7 - - + +
83A GLN* 4.6 8.9 - - - +
84A TYR* 3.0 45.8 + - + +
183A GLN* 3.7 25.9 + - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU 3.0 17.4 + - - +
60A VAL 3.6 4.3 - - - +
62A ARG* 1.3 76.0 - - - +
64A TRP* 1.3 62.1 + - - +
65A THR 3.3 0.5 + - - -
66A ASP 3.5 6.6 + - - +
67A PRO* 4.5 0.5 - - - +
69A PHE* 4.0 8.1 - - + -
70A ARG* 3.3 45.1 - - + +
73A LEU* 3.9 22.0 - - + -
171A LEU* 4.0 13.5 - - + -
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Residues in contact with TRP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 2.9 32.7 + - + +
61A ALA* 3.6 7.9 - - - +
62A ARG 3.2 0.2 - - - -
63A ALA* 1.3 77.3 - - - +
65A THR* 1.3 60.1 + - + +
66A ASP 3.6 0.2 - - - -
67A PRO* 5.9 0.2 - - - +
70A ARG* 5.3 7.4 - - - +
171A LEU* 4.1 10.2 - - + +
172A PRO* 2.9 23.3 + - + -
173A GLN 3.5 19.1 - - - -
174A ARG* 3.2 50.1 + - + +
175A PRO* 3.9 13.9 - - + -
186A LEU* 3.9 40.2 - - + -
189A ILE* 4.4 5.8 - - + -
190A VAL* 3.6 28.0 - - + -
201A PRO* 4.0 14.4 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 12.8 + - - +
62A ARG 3.1 5.0 + - - -
64A TRP* 1.3 79.9 - - - +
66A ASP* 1.3 59.4 + - - +
67A PRO* 3.8 8.8 - - - +
174A ARG* 3.9 9.2 - - - +
181A TRP 4.7 7.0 - - - +
183A GLN* 3.5 28.4 + - + +
186A LEU* 3.5 31.2 - - + -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 2.9 51.6 + - - +
63A ALA 3.5 6.8 + - - +
64A TRP 3.6 0.2 - - - -
65A THR* 1.3 81.8 - - - +
67A PRO* 1.4 66.8 - - - +
68A GLU* 3.1 13.7 + - - +
69A PHE* 3.0 21.4 + - + +
70A ARG 2.9 19.1 + - - -
183A GLN* 5.9 0.4 - - - +
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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