Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 2PI8
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 GLN 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.2 17.7 + - + +
54A TYR 3.8 1.3 - - - -
56A ASN* 1.3 94.4 - - + +
58A SER* 1.3 64.6 + - - +
59A ASN 3.2 2.5 - - - -
60A VAL* 3.2 35.5 + - - +
61A TYR* 3.0 46.5 + - + +
267A PRO 5.0 1.3 - - - +
268A GLY* 3.3 30.8 + - - +
269A THR* 4.2 8.6 + - - +
270A THR 4.6 0.2 - - - +
333A LEU 5.3 0.6 + - - -
334A LYS* 6.0 1.8 - - - +
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Residues in contact with SER 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 TYR* 2.9 36.0 + - - -
55A GLY* 4.0 11.9 + - - -
56A ASN 3.5 1.2 - - - -
57A GLN* 1.3 77.9 - - - +
59A ASN* 1.3 63.2 + - - +
61A TYR* 3.4 6.4 + - - +
62A ASN* 2.7 45.3 + - - +
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Residues in contact with ASN 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 GLY 4.5 4.9 - - - +
56A ASN 4.4 8.2 - - - +
57A GLN 5.0 0.4 - - - -
58A SER* 1.3 85.7 + - - +
60A VAL* 1.3 58.5 + - + +
62A ASN* 3.5 4.5 + - - +
63A ALA* 2.9 30.7 + - - +
335A THR* 3.6 20.3 - - + +
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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
----------------------------------------------------------
56A ASN 5.3 0.9 - - - +
57A GLN* 3.2 38.9 + - - +
59A ASN* 1.3 75.8 - - + +
61A TYR* 1.3 65.6 + - + +
63A ALA* 3.4 3.6 + - - +
64A VAL* 3.3 23.0 + - - +
270A THR* 3.4 21.3 - - + +
333A LEU* 3.1 28.9 - - + +
334A LYS* 4.2 9.4 - - + -
335A THR* 3.9 26.0 - - + +
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Residues in contact with TYR 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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39A PHE* 5.1 1.1 - + - -
43A ILE* 3.7 35.4 - - + -
46A ILE* 3.4 30.3 - - + +
53A LEU* 4.6 1.0 - - - +
54A TYR* 3.6 38.4 - + + +
57A GLN* 3.0 35.2 + - + +
58A SER 3.8 3.6 - - - +
60A VAL* 1.3 76.1 - - - +
62A ASN* 1.3 60.6 + - - +
64A VAL* 3.3 10.3 - - - +
65A GLN* 3.2 30.5 + - - +
268A GLY* 2.7 43.4 + - - -
270A THR* 3.5 19.3 - - - -
294A VAL* 4.7 3.6 - - + -
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Residues in contact with ASN 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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47A ARG* 5.5 1.6 + - - -
54A TYR* 4.4 12.8 + - - -
58A SER* 2.7 43.0 + - - +
59A ASN* 4.0 5.3 - - - +
61A TYR* 1.3 75.0 - - - +
63A ALA* 1.3 62.7 + - - +
65A GLN* 3.1 18.1 + - - +
66A GLU* 2.8 38.2 - - - +
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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 ASN 2.9 18.5 + - - +
60A VAL* 3.5 10.3 - - + +
61A TYR 3.3 0.2 - - - -
62A ASN* 1.3 79.1 - - - +
64A VAL* 1.3 59.4 + - + +
65A GLN 3.5 0.2 + - - -
66A GLU* 3.7 9.1 + - - +
67A TRP 3.8 4.2 + - - -
80A PHE* 3.8 14.4 - - - +
81A GLY 3.7 23.1 - - - +
82A ILE* 3.4 19.0 - - + +
334A LYS 5.3 1.8 - - - +
335A THR* 4.2 8.1 - - + -
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Residues in contact with VAL 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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39A PHE* 3.6 27.1 - - + -
60A VAL 3.3 11.2 + - - +
61A TYR* 3.3 18.4 - - - +
63A ALA* 1.3 76.5 - - - +
65A GLN* 1.3 62.7 + - - +
66A GLU 3.3 1.1 - - - -
67A TRP* 3.4 24.6 + - + +
68A LEU* 3.2 22.6 + - - +
82A ILE* 3.8 12.3 - - + +
270A THR* 4.6 4.9 - - + -
292A LEU* 4.0 17.3 - - + -
333A LEU* 4.0 24.0 - - + -
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Residues in contact with GLN 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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39A PHE* 4.6 8.0 - - - -
40A ALA* 4.6 15.7 + - - +
43A ILE* 4.0 25.6 - - - +
61A TYR 3.2 19.4 + - - +
62A ASN* 3.1 25.7 + - - +
64A VAL* 1.3 79.4 - - - +
66A GLU* 1.3 64.4 + - - +
68A LEU* 3.2 29.9 - - + +
69A ARG* 3.2 43.3 + - - +
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Residues in contact with GLU 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 ASN* 2.8 34.1 + - - +
63A ALA* 3.7 7.6 + - - +
64A VAL 3.3 0.2 - - - -
65A GLN* 1.3 86.8 - - - +
67A TRP* 1.3 65.1 - - - +
69A ARG* 3.5 9.3 + - + +
70A ALA* 3.3 18.0 + - - +
80A PHE* 3.4 30.2 - - + +
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Residues in contact with TRP 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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33A PRO* 3.8 22.0 - - + -
63A ALA 3.8 1.2 + - - -
64A VAL* 3.4 25.9 + - + +
65A GLN 3.4 0.2 - - - -
66A GLU* 1.3 79.8 - - - +
68A LEU* 1.3 65.6 + - + +
70A ALA* 4.1 1.7 - - - +
71A GLY 3.2 26.7 + - - -
72A GLY* 3.2 33.6 + - - -
73A ASP 2.9 32.5 + - - +
74A THR* 3.8 7.9 - - + -
76A ASN 3.0 16.7 + - - -
77A MSE 3.4 25.8 - - + +
80A PHE* 3.6 26.6 - + + -
82A ILE* 3.6 19.7 - - + -
272A ILE* 3.7 25.4 - - + -
292A LEU* 4.1 14.4 - - + -
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Residues in contact with LEU 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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33A PRO* 6.2 2.9 - - + -
36A ALA* 4.1 35.7 - - + +
39A PHE* 4.2 8.3 - - + -
40A ALA* 6.1 2.0 - - + -
64A VAL 3.2 15.3 - - - +
65A GLN* 3.2 31.6 - - + +
67A TRP* 1.3 84.8 - - + +
69A ARG* 1.3 91.5 + - + +
70A ALA 4.0 0.5 - - - -
71A GLY* 3.0 21.8 + - - +
72A GLY* 4.5 2.5 - - - -
292A LEU* 4.1 23.6 - - + -
34C ILE* 5.0 5.6 - - + +
289C GLU* 4.3 5.7 - - - +
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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
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65A GLN* 3.2 38.2 + - - +
66A GLU* 3.5 14.1 + - + +
67A TRP 3.3 0.6 - - - -
68A LEU* 1.3 87.9 - - - +
70A ALA* 1.3 61.3 + - - +
255C ARG* 5.4 8.0 - - - +
277C LEU* 3.5 18.6 - - + +
289C GLU* 3.2 21.8 - - - +
320C ARG* 5.2 11.5 - - - +
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Residues in contact with ALA 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 GLU 3.3 12.7 + - - +
67A TRP 4.1 2.2 - - - +
68A LEU 4.0 0.4 - - - -
69A ARG* 1.3 84.2 - - - +
71A GLY* 1.3 59.4 + - - +
80A PHE* 4.1 18.4 - - + -
277C LEU* 3.6 11.3 - - - +
287C GLN* 3.2 22.7 - - + +
288C TYR 3.3 21.1 - - - +
289C GLU* 4.1 9.7 - - - +
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Residues in contact with GLY 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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33A PRO* 5.5 0.3 - - - +
67A TRP 3.2 5.9 + - - -
68A LEU* 3.0 21.9 - - - +
70A ALA* 1.3 83.2 - - - +
72A GLY* 1.3 57.8 + - - +
80A PHE* 5.6 0.2 - - - -
34C ILE* 3.0 28.2 - - - +
289C GLU* 6.0 0.4 - - - -
290C LEU 6.2 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