Contacts of the helix formed by residues 61 - 69 (chain A) in PDB entry 3ZPL
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 MET 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ARG* 1.3 70.8 - - - +
62A THR* 1.3 63.5 + - - +
64A LEU* 3.0 3.9 + - - -
65A ALA* 2.9 20.0 + - - -
72A ARG* 5.8 4.3 - - + +
75A LEU* 2.9 40.3 - - + +
76A SER* 4.7 1.1 - - - -
79A VAL* 3.9 25.4 - - + -
90A ARG* 5.3 1.6 - - - -
100A GLN* 3.2 29.5 + - + +
101A PHE 4.4 2.7 - - - +
102A ALA* 4.0 23.8 - - + -
5C A 3.6 24.3 + - - +
6C T 3.4 30.3 - - - +
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Residues in contact with THR 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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60A ARG 3.4 0.2 - - - -
61A MET* 1.3 73.0 - - - +
63A GLU* 1.3 58.6 + - - +
65A ALA* 3.2 6.8 + - - +
66A LYS* 2.8 28.9 + - + +
72A ARG* 3.9 19.3 - - - +
161A TRP* 4.0 32.0 - - + +
162A LEU* 5.2 4.9 - - + -
4C G 4.0 20.5 + - - +
5C A 2.9 25.6 + - - -
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Residues in contact with GLU 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* 3.9 21.5 - - + +
60A ARG* 3.0 45.1 + - + +
62A THR* 1.3 79.4 - - - +
64A LEU* 1.3 62.5 + - - +
66A LYS* 3.2 8.6 + - - +
67A TYR* 3.1 36.5 + - + -
101A PHE* 5.7 0.9 - - - -
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Residues in contact with LEU 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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47A LEU* 4.1 29.6 - - + +
50A LYS* 4.3 11.4 - - + -
51A LEU* 3.9 27.8 - - + -
59A LEU* 4.1 24.8 - - + +
60A ARG 3.0 11.0 + - - +
61A MET* 3.0 9.6 + - - +
63A GLU* 1.3 78.8 - - - +
65A ALA* 1.3 62.2 + - - +
67A TYR* 3.2 2.1 + - + +
68A ALA* 3.0 25.0 + - + +
75A LEU* 3.8 26.0 - - + -
79A VAL* 4.8 3.6 - - + -
102A ALA* 3.9 20.0 - - + -
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Residues in contact with ALA 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 MET 2.9 12.0 + - - +
62A THR* 3.5 11.2 - - - +
64A LEU* 1.3 76.1 - - - +
66A LYS* 1.3 51.0 + - - +
68A ALA* 3.3 0.7 + - - -
69A LYS* 2.7 31.5 + - - -
70A ILE* 3.2 37.8 + - + +
71A THR 4.3 8.3 - - - -
72A ARG* 4.3 4.5 - - + +
75A LEU* 3.5 14.4 - - + +
161A TRP* 3.8 9.6 - - + -
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Residues in contact with LYS 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 THR* 2.8 20.7 + - + +
63A GLU* 3.2 8.9 + - - +
65A ALA* 1.3 72.0 - - - +
67A TYR* 1.3 60.8 + - + +
69A LYS* 3.0 38.9 + - - +
161A TRP* 3.6 46.5 - - + +
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Residues in contact with TYR 67 (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 LYS* 3.6 49.3 + - + -
59A LEU* 3.7 27.5 - - + +
63A GLU* 3.1 31.2 + - + -
64A LEU* 3.7 4.9 - - + +
66A LYS* 1.3 78.1 - - + +
68A ALA* 1.3 61.7 + - - +
69A LYS* 3.4 3.9 + - - +
17B ARG* 2.9 45.5 + - - +
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Residues in contact with ALA 68 (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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43A VAL* 5.4 3.4 - - + +
46A GLY 6.3 0.4 - - - -
47A LEU* 3.7 27.1 - - + -
64A LEU* 3.0 17.2 + - + +
65A ALA 3.8 3.4 - - - +
67A TYR* 1.3 74.9 - - - +
69A LYS* 1.3 70.8 + - - +
70A ILE* 3.5 23.2 - - + +
20B ILE* 6.0 2.1 - - - +
24B THR* 4.1 8.7 + - - +
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Residues in contact with LYS 69 (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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65A ALA 2.7 14.3 + - - -
66A LYS* 3.0 27.7 + - - +
67A TYR* 3.2 13.3 - - - +
68A ALA* 1.3 78.4 - - - +
70A ILE* 1.3 57.5 + - - +
74A ARG* 5.6 0.2 + - - -
151A GLN* 2.9 37.4 + - - +
160A PRO* 3.7 15.8 - - - +
161A TRP* 3.8 15.4 - - + -
17B ARG* 3.7 25.5 - - - +
21B GLU* 4.3 20.2 - - - -
24B THR* 3.7 23.7 - - + +
25B LEU* 4.1 20.7 - - + +
28B ASP* 5.4 1.9 - - - +
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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