Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 4PGF
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 THR 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS 2.7 16.8 + - - +
56A MET* 1.3 83.8 - - - +
58A VAL* 1.3 64.7 + - - +
59A GLU* 2.9 13.3 + - - -
60A THR* 3.3 7.0 + - - -
61A ALA 3.0 18.0 + - - -
83A SER 3.7 14.8 - - - +
85A GLN* 3.3 30.3 - - - +
88A ALA* 3.5 6.7 - - - +
347A LEU* 3.9 11.7 - - + -
502A ADN 2.8 30.5 + - + +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.7 26.5 - - + +
22A LEU* 4.0 6.3 - - + -
25A ALA* 3.6 26.9 - - + -
57A THR* 1.3 75.6 - - - +
59A GLU* 1.3 71.7 + - - +
61A ALA* 3.3 18.4 - - - +
62A VAL* 3.3 10.0 + - - +
85A GLN* 3.0 15.0 + - - +
87A HIS* 3.9 23.1 - - + +
88A ALA* 3.6 12.3 - - + +
351A MET* 4.8 4.0 - - + -
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 5.4 0.2 - - - +
29A MET* 4.0 10.4 - - + +
57A THR* 2.9 17.0 + - - +
58A VAL* 1.3 88.7 + - - +
60A THR* 1.3 62.0 + - - +
62A VAL* 3.2 7.5 + - - +
63A LEU 3.1 16.1 + - - -
85A GLN* 4.6 0.9 - - - +
351A MET* 4.2 4.7 - - - +
353A HIS 3.9 8.1 - - - +
354A PRO* 4.8 0.3 - - - +
355A SER* 3.4 43.9 + - - -
358A MET* 3.8 15.3 - - + -
362A PHE* 3.4 22.7 - - + -
502A ADN 2.8 27.3 + - - +
208B ASP* 5.5 4.0 - - - +
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Residues in contact with THR 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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54A LEU* 3.4 17.2 - - + +
55A HIS 2.6 27.2 + - - +
56A MET* 4.3 2.2 - - + -
57A THR* 3.3 13.7 + - - -
59A GLU* 1.3 74.2 - - - +
61A ALA* 1.3 55.9 - - - +
63A LEU* 3.1 6.1 + - + +
64A ILE* 2.8 38.3 + - + +
76A TRP* 3.4 43.5 - - + +
362A PHE* 3.6 7.2 - - - -
502A ADN 3.5 4.9 - - - -
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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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22A LEU* 3.6 24.5 - - + -
56A MET* 3.7 6.4 - - + +
57A THR 3.0 13.1 + - - +
58A VAL* 3.3 12.1 - - - +
60A THR* 1.3 76.5 - - - +
62A VAL* 1.3 61.0 + - - +
64A ILE* 3.1 3.9 + - - +
65A GLU* 3.0 25.3 + - - +
88A ALA 4.3 2.9 - - - +
92A ILE* 3.6 32.8 - - + +
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.2 17.7 - - + +
25A ALA* 4.0 23.1 - - + -
26A GLU* 4.1 18.8 - - + +
29A MET* 3.9 13.7 - - + -
32A LEU* 3.8 22.4 - - + -
33A MET* 4.8 1.8 - - - -
36A ARG* 3.0 24.5 + - - +
58A VAL 3.4 15.0 - - - +
59A GLU 3.4 7.2 - - - +
60A THR 3.2 0.4 - - - -
61A ALA* 1.3 75.4 - - - +
63A LEU* 1.3 60.6 + - - +
65A GLU* 4.7 3.1 - - - -
66A THR* 2.8 22.4 + - - -
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Residues in contact with LEU 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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32A LEU* 3.9 7.5 - - + +
54A LEU* 5.0 0.7 - - + -
59A GLU 3.1 4.9 + - - -
60A THR* 3.1 9.5 + - + +
62A VAL* 1.3 74.1 - - - +
64A ILE* 1.3 65.9 + - - +
66A THR* 3.2 4.6 + - - -
67A LEU* 3.2 30.8 + - + +
76A TRP* 4.3 24.5 - - + -
129A LEU* 4.4 11.4 - - + -
362A PHE* 3.6 57.7 - - + +
365A GLN* 4.6 7.0 - - + -
366A VAL* 3.5 29.2 - - + -
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Residues in contact with ILE 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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56A MET* 3.9 25.4 - - + -
60A THR* 2.8 22.8 + - + +
61A ALA 3.1 5.6 + - - +
63A LEU* 1.3 73.2 - - - +
65A GLU* 1.3 58.9 + - - +
67A LEU* 3.0 26.9 + - - +
68A VAL* 3.1 11.6 + - - +
74A VAL* 4.1 10.9 - - + +
76A TRP* 3.7 50.0 - - + -
92A ILE* 3.9 12.8 - - + -
97A ILE* 3.7 37.5 - - + -
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Residues in contact with GLU 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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19A ARG* 2.8 43.0 + - - -
22A LEU* 3.9 12.8 - - - +
26A GLU* 3.7 13.2 - - - +
36A ARG* 3.1 18.5 + - - +
61A ALA 3.0 14.5 + - - +
62A VAL* 4.7 1.6 - - - -
64A ILE* 1.3 76.1 - - - +
66A THR* 1.3 55.7 + - - +
67A LEU 3.4 0.2 - - - -
68A VAL* 3.8 9.6 - - - +
69A THR* 2.9 31.5 + - - -
92A ILE* 4.1 11.8 - - + +
95A ALA* 4.5 7.7 - - + +
97A ILE* 4.4 9.2 - - + -
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Residues in contact with THR 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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32A LEU* 3.8 32.1 - - + +
35A MET* 4.3 9.6 - - + -
36A ARG* 2.9 26.9 + - + +
62A VAL 2.8 18.5 + - - -
63A LEU* 3.4 11.9 - - - -
64A ILE 3.1 0.6 - - - -
65A GLU* 1.3 76.9 - - - +
67A LEU* 1.3 59.8 + - - +
69A THR* 3.4 1.4 + - - -
70A LEU* 3.0 34.1 + - + +
366A VAL* 4.1 22.2 - - + -
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Residues in contact with LEU 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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45A LEU* 3.7 23.6 - - + -
50A ILE* 4.2 17.3 - - + -
63A LEU* 3.2 20.1 + - + +
64A ILE* 3.0 9.5 + - - +
66A THR* 1.3 76.7 - - - +
68A VAL* 1.3 60.1 + - - +
70A LEU* 3.3 9.6 + - - +
71A GLY 3.4 0.3 + - - -
72A ALA* 3.0 27.4 + - - +
74A VAL* 3.8 19.1 - - + -
76A TRP* 4.2 18.2 - - + -
129A LEU* 4.1 21.8 - - + -
366A VAL* 4.2 27.4 - - + -
369A GLN* 4.6 7.9 - - + -
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Residues in contact with VAL 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 LYS* 5.1 2.4 - - - -
64A ILE 3.1 13.6 + - - +
65A GLU* 3.8 8.5 - - + +
67A LEU* 1.3 73.7 - - - +
69A THR* 1.3 57.1 - - - +
70A LEU 3.0 1.1 - - - -
71A GLY* 2.6 27.2 + - - -
72A ALA 3.6 13.5 + - - +
74A VAL* 3.9 18.8 - - + +
97A ILE* 4.0 27.8 - - + -
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Residues in contact with THR 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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36A ARG* 4.2 28.1 + - + -
40A SER* 3.4 35.6 - - - +
43A LYS* 3.6 19.6 + - - +
65A GLU 2.9 21.2 + - - -
66A THR 3.4 6.0 + - - -
68A VAL* 1.3 76.8 - - - +
70A LEU* 1.3 59.3 + - + +
71A GLY 3.1 3.2 + - - -
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Residues in contact with LEU 70 (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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35A MET* 3.8 12.6 - - + +
36A ARG* 4.3 10.1 - - - -
39A TYR* 3.6 34.1 - - + -
43A LYS* 3.2 15.2 - - - +
44A PRO* 3.9 3.6 - - + -
45A LEU* 2.8 50.4 + - + +
66A THR* 3.0 23.1 + - + +
67A LEU 3.6 1.1 - - - +
68A VAL 3.0 1.6 - - - -
69A THR* 1.3 81.4 - - + +
71A GLY* 1.3 57.1 + - - +
72A ALA 3.5 1.8 - - - -
366A VAL* 3.6 32.1 - - + -
370A ILE* 3.8 17.9 - - + -
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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