Contacts of the helix formed by residues 57 - 78 (chain A) in PDB entry 4PIM
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 TYR 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO 5.6 0.9 - - - +
55A GLU 3.1 15.3 + - - +
56A TYR* 1.3 71.2 - - - +
58A PRO* 1.4 77.0 - - + +
59A THR 3.2 0.6 + - - -
60A ARG* 3.5 16.4 + - + +
61A THR* 2.6 40.6 + - - +
194A ASP* 2.6 40.6 + - - -
197A LYS* 2.9 35.1 + - + -
201A ARG* 3.9 35.9 - - + +
202A LEU* 3.3 15.5 - - + +
205A ALA* 3.9 18.1 - - + +
206A TYR* 5.5 0.7 - + - -
286A LYS* 4.6 0.2 + - - -
313A ASP* 4.3 6.5 - - + +
314A PHE* 5.3 0.4 - + - -
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 3.2 41.1 - - + +
57A TYR* 1.4 119.0 - - + +
59A THR* 1.3 62.5 + - - +
61A THR* 3.7 1.6 - - - +
62A GLU* 2.9 28.0 + - - +
161A GLY* 5.1 6.3 - - - +
194A ASP* 3.8 12.8 - - + +
205A ALA* 5.0 0.9 - - + -
206A TYR* 4.9 3.4 - - + +
286A LYS* 5.3 0.2 - - - +
314A PHE* 4.3 22.9 - - + -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.4 39.8 - - + +
56A TYR* 3.4 21.3 + - - -
57A TYR 3.3 0.8 - - - -
58A PRO* 1.3 78.4 - - - +
60A ARG* 1.3 59.1 + - - +
62A GLU* 3.9 4.2 - - - +
63A ALA* 2.9 31.4 + - + +
91A GLU* 5.7 5.2 - - + +
92A LYS* 4.7 23.3 + - + +
161A GLY* 6.6 0.2 - - - -
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR 4.2 3.4 + - - -
52A ARG* 3.6 17.8 + - - +
53A LEU 2.8 26.6 + - - -
54A PRO* 3.0 30.5 + - - +
56A TYR 3.3 19.5 + - - -
57A TYR* 3.6 15.5 - - + +
59A THR* 1.3 79.4 - - - +
61A THR* 1.3 62.1 + - - +
63A ALA* 3.7 7.3 - - - +
64A GLN* 3.0 29.1 + - - +
67A ARG* 5.0 1.4 + - - -
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.6 37.5 + - - +
58A PRO* 3.7 3.4 - - - -
60A ARG* 1.3 78.4 - - - +
62A GLU* 1.3 65.1 + - - +
64A GLN* 3.3 6.8 + - - +
65A ILE* 3.1 23.0 + - + +
309A ASP* 3.4 40.1 - - + +
313A ASP* 4.1 8.6 + - + +
314A PHE* 3.6 16.4 - - + -
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 2.9 16.8 + - - +
59A THR* 3.9 2.8 - - - +
61A THR* 1.3 76.2 - - - +
63A ALA* 1.3 63.7 + - - +
65A ILE* 3.1 7.0 + - - +
66A LEU* 3.0 25.7 + - + +
92A LYS* 2.6 37.8 + - + -
160A LEU* 3.3 21.1 - - - +
161A GLY* 2.9 28.6 + - - -
192A GLY* 3.7 0.9 - - - -
314A PHE* 3.3 36.8 - - + -
316A LEU* 3.7 15.0 - - + +
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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
----------------------------------------------------------
59A THR* 2.9 21.0 + - + +
60A ARG* 3.7 8.7 - - - +
62A GLU* 1.3 77.6 - - - +
64A GLN* 1.3 57.1 + - - +
66A LEU* 3.3 3.1 + - - -
67A ARG* 2.7 47.5 + - - +
91A GLU* 4.7 10.5 - - - +
92A LYS* 4.4 20.1 - - + +
95A MSE 3.6 9.1 - - + +
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Residues in contact with GLN 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 ARG 3.0 18.3 + - - +
61A THR* 3.7 6.1 - - - +
63A ALA* 1.3 72.5 - - - +
65A ILE* 1.3 66.7 + - + +
67A ARG* 2.7 40.7 + - - +
68A THR* 3.1 48.5 + - + +
309A ASP* 6.2 4.0 - - + -
310A PRO* 6.4 2.5 - - + -
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Residues in contact with ILE 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 THR 3.1 16.5 + - - +
62A GLU* 3.1 6.5 + - - +
64A GLN* 1.3 78.8 - - + +
66A LEU* 1.3 61.7 + - - +
68A THR* 3.3 6.4 + - - -
69A ARG* 3.0 26.6 + - + +
73A ILE* 5.5 1.1 - - + -
307A TRP* 3.8 28.5 - - + +
308A THR* 4.1 4.3 - - - +
309A ASP* 3.7 28.0 - - + +
314A PHE* 3.7 42.0 - - + +
315A GLY* 4.7 0.9 - - - +
316A LEU* 3.6 20.9 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.0 18.5 + - + +
63A ALA 3.7 6.1 - - - +
65A ILE* 1.3 76.7 - - - +
67A ARG* 1.3 63.1 + - - +
70A SER* 2.9 32.3 + - - +
73A ILE* 3.7 26.0 - - + -
92A LYS* 3.6 49.4 - - + +
95A MSE 3.7 14.3 - - + +
96A LEU* 4.1 18.4 - - + -
160A LEU* 4.3 11.4 - - + -
190A LEU* 4.4 7.2 - - + -
316A LEU* 3.7 15.7 - - + -
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 5.0 1.2 + - - -
63A ALA* 2.7 28.3 + - - +
64A GLN* 2.7 58.5 + - - +
65A ILE 3.3 0.6 - - - -
66A LEU* 1.3 74.5 - - - +
68A THR* 1.3 63.2 + - + +
70A SER* 4.6 5.0 + - - -
91A GLU* 4.3 12.1 + - - -
95A MSE 3.4 34.2 - - + +
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Residues in contact with THR 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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64A GLN* 3.1 41.3 + - - +
65A ILE* 3.3 8.7 + - - -
66A LEU 3.1 0.2 - - - -
67A ARG* 1.3 85.2 - - + +
69A ARG* 1.3 74.0 + - - +
70A SER 3.8 0.4 - - - -
71A ALA 5.6 0.2 + - - -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.0 16.9 + - + +
66A LEU 3.9 0.2 - - - -
68A THR* 1.3 97.2 + - - +
70A SER* 1.3 63.8 + - - +
71A ALA* 3.2 3.6 - - - +
72A GLU* 3.0 36.6 + - - +
73A ILE* 2.9 28.7 + - + +
307A TRP* 3.7 29.4 - - + +
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Residues in contact with SER 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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66A LEU* 2.9 21.6 + - - -
67A ARG 4.6 4.7 + - - -
68A THR 3.8 1.0 - - - -
69A ARG* 1.3 76.0 - - - +
71A ALA* 1.3 65.8 + - - +
73A ILE* 3.3 12.3 + - - +
74A ILE* 3.0 28.6 + - - +
95A MSE 4.0 26.6 + - - +
96A LEU* 4.7 7.2 - - - -
99A ALA* 3.8 12.0 - - - +
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Residues in contact with ALA 71 (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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68A THR 5.6 0.2 - - - -
69A ARG 3.2 1.2 - - - -
70A SER* 1.3 83.5 + - - +
72A GLU* 1.3 56.3 + - - +
74A ILE* 3.5 3.0 + - - +
75A SER* 2.9 29.5 + - - -
99A ALA* 4.4 9.2 - - + -
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Residues in contact with GLU 72 (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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69A ARG* 3.0 41.6 + - - +
71A ALA* 1.3 75.1 - - - +
73A ILE* 1.3 60.9 + - - +
75A SER* 3.4 6.8 + - - -
76A ALA* 2.9 31.1 + - + +
305A HIS* 4.1 17.9 + - + +
307A TRP* 2.7 35.0 + - + +
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Residues in contact with ILE 73 (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 ILE 5.2 0.2 - - - +
66A LEU* 3.7 30.7 - - + -
69A ARG* 2.9 28.5 + - + +
70A SER* 3.3 8.9 + - - +
72A GLU* 1.3 77.1 - - - +
74A ILE* 1.3 59.8 + - + +
76A ALA* 3.2 3.8 + - - +
77A ALA* 2.9 27.7 + - - +
96A LEU* 4.2 10.1 - - + -
156A LEU* 4.7 6.5 - - + -
190A LEU* 4.0 30.7 - - + -
307A TRP* 3.6 40.2 - - + -
316A LEU* 4.7 5.4 - - + -
318A LEU* 4.6 5.6 - - + +
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Residues in contact with ILE 74 (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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70A SER 3.0 19.3 + - - +
71A ALA* 3.9 3.8 - - - +
73A ILE* 1.3 73.4 - - - +
75A SER* 1.3 61.8 + - - +
77A ALA* 3.9 2.7 - - + +
78A GLY* 2.9 28.2 + - - -
79A ALA 4.4 1.9 + - - +
96A LEU* 3.9 17.9 - - + +
99A ALA* 3.4 37.9 - - + +
100A MSE 3.4 33.9 - - + -
103A ALA* 4.3 5.4 - - + -
105A LEU* 4.2 17.0 - - + +
156A LEU* 3.9 25.6 - - + -
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Residues in contact with SER 75 (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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71A ALA 2.9 18.1 + - - -
72A GLU* 3.7 7.6 - - - -
74A ILE* 1.3 78.7 - - - +
76A ALA* 1.3 63.6 + - - +
77A ALA 3.4 0.2 + - - -
78A GLY* 3.6 8.3 + - - -
103A ALA* 6.5 0.4 - - - -
105A LEU* 5.9 1.6 - - - -
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Residues in contact with ALA 76 (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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72A GLU* 2.9 19.1 + - + +
73A ILE* 3.5 6.7 - - - +
75A SER* 1.3 79.2 - - - +
77A ALA* 1.3 60.7 + - - +
154A ARG* 5.1 3.6 + - - -
188A SER* 5.0 0.9 + - - -
305A HIS* 3.6 34.1 - - + +
307A TRP* 4.8 0.9 - - + -
318A LEU* 3.8 16.6 - - + +
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Residues in contact with ALA 77 (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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73A ILE 2.9 16.8 + - - +
74A ILE* 4.0 4.0 - - + +
75A SER 3.3 0.2 - - - -
76A ALA* 1.3 78.7 - - - +
78A GLY* 1.3 64.4 + - - +
79A ALA* 3.1 14.6 + - + +
154A ARG* 3.2 21.2 + - - -
156A LEU* 4.1 30.7 - - + -
186A GLY 4.2 1.6 - - - +
188A SER* 3.9 20.4 + - - +
318A LEU* 4.2 4.5 - - + +
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 2.9 14.9 + - - -
75A SER 3.6 6.5 + - - -
76A ALA 3.5 2.0 - - - -
77A ALA* 1.3 76.4 - - - +
79A ALA* 1.3 60.7 + - - +
80A ASP 4.1 0.3 + - - -
105A LEU* 4.5 18.1 - - - +
154A ARG* 3.2 21.9 + - - +
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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
------------------------------------------------------------
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