Contacts of the helix formed by residues 57 - 71 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.4 13.5 + - + +
54D TYR 3.0 5.0 + - - -
56D ASN* 1.3 96.3 + - + +
58D SER* 1.3 62.6 + - - +
59D ASN* 3.5 4.3 - - - -
60D VAL* 3.3 28.0 + - + +
61D TYR* 3.0 50.2 + - + +
268D GLY* 3.6 25.9 - - - +
269D THR* 5.5 2.6 - - - +
270D THR 5.6 0.7 + - - -
333D LEU 5.5 0.3 - - - +
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Residues in contact with SER 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D TYR* 2.7 42.2 + - - -
55D GLY* 3.3 18.5 + - - -
56D ASN 3.6 2.2 - - - -
57D GLN* 1.3 78.2 - - - +
59D ASN* 1.3 59.2 + - - +
61D TYR* 3.2 1.4 + - - +
62D ASN* 2.8 45.2 + - - +
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Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASN 4.2 6.9 - - - +
57D GLN 3.9 0.7 - - - -
58D SER* 1.3 81.5 + - - +
60D VAL* 1.3 75.1 + - - +
62D ASN* 4.0 7.9 - - - +
63D ALA* 3.2 25.5 + - - +
335D THR* 3.6 22.0 + - + +
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ASN 5.1 0.4 - - - +
57D GLN* 3.3 31.0 - - + +
58D SER 3.2 0.6 - - - -
59D ASN* 1.3 92.7 + - - +
61D TYR* 1.3 63.7 + - - +
63D ALA* 3.4 2.9 + - - +
64D VAL* 3.3 26.3 + - + +
270D THR* 3.7 23.1 - - + +
333D LEU* 3.7 26.5 - - + +
334D LYS* 4.9 2.7 - - - -
335D THR* 3.6 28.7 - - + +
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Residues in contact with TYR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PHE* 4.7 2.9 - + - -
43D ILE* 3.5 52.5 - - + -
46D ILE* 3.6 23.8 - - + +
53D LEU 4.9 0.3 + - - -
54D TYR* 3.8 28.0 - + + -
57D GLN* 3.0 33.3 + - + +
58D SER 3.7 2.5 - - - +
60D VAL* 1.3 74.3 - - + +
62D ASN* 1.3 66.4 + - - +
64D VAL* 3.1 15.5 - - - +
65D GLN* 3.1 22.2 + - + +
268D GLY* 2.7 33.2 + - - -
270D THR* 3.1 27.6 - - - -
294D VAL* 3.8 3.1 - - + +
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ARG* 5.3 1.6 + - - -
54D TYR* 3.9 16.5 + - - -
58D SER* 2.8 36.2 + - - +
59D ASN* 4.0 6.9 - - - +
61D TYR* 1.3 78.4 - - - +
63D ALA* 1.3 62.2 + - - +
65D GLN* 3.6 17.9 - - - +
66D GLU* 3.7 8.1 + - - +
80D PHE* 4.5 2.6 - - - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN 3.2 20.9 + - - +
60D VAL 3.6 5.4 - - - +
61D TYR 3.2 0.2 - - - -
62D ASN* 1.3 75.5 - - - +
64D VAL* 1.3 65.6 + - - +
65D GLN 3.2 0.7 + - - -
66D GLU 3.3 9.7 + - - -
67D TRP* 3.4 9.4 + - - +
80D PHE* 3.5 35.9 - - + +
82D ILE* 3.9 10.3 - - + +
335D THR* 3.6 17.5 - - + -
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PHE* 3.5 32.3 - - + -
60D VAL* 3.3 15.0 + - + +
61D TYR* 3.1 20.0 - - - +
63D ALA* 1.3 75.7 - - - +
65D GLN* 1.3 57.5 + - + +
67D TRP* 3.3 13.5 + - + +
68D LEU* 3.0 33.1 + - - +
82D ILE* 3.9 23.6 - - + -
270D THR* 4.8 6.5 - - + -
292D LEU* 5.1 2.9 - - + -
333D LEU* 4.0 29.4 - - + -
335D THR* 6.2 0.4 - - + -
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA 5.3 0.2 - - - +
39D PHE* 3.6 31.3 - - - -
40D ALA* 3.8 29.3 - - - +
43D ILE* 4.6 7.4 - - + +
61D TYR* 3.1 20.1 + - + +
62D ASN* 3.6 13.0 - - - +
63D ALA 3.1 0.8 - - - -
64D VAL* 1.3 79.2 - - - +
66D GLU* 1.3 57.8 + - - +
68D LEU* 3.3 9.5 + - - +
69D ARG* 3.0 52.4 + - + +
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLN* 3.0 37.7 + - - +
62D ASN 3.7 5.2 + - - +
63D ALA 3.3 5.0 + - - +
65D GLN* 1.3 76.6 - - - +
67D TRP* 1.3 60.5 - - - +
69D ARG* 4.1 1.9 - - - +
70D ALA* 2.9 38.1 + - + +
80D PHE* 3.6 41.2 - - + -
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Residues in contact with TRP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO* 4.0 6.3 - - + -
63D ALA 3.4 2.9 + - - +
64D VAL* 3.4 26.9 - - + +
66D GLU* 1.3 80.8 - - - +
68D LEU* 1.3 66.5 + - + +
70D ALA* 4.1 4.0 - - - +
71D GLY 3.3 6.4 + - - -
72D GLY* 2.9 49.6 + - - -
73D ASP 2.9 23.9 + - - -
74D THR* 4.1 3.6 - - + -
76D ASN* 3.3 29.2 - - + +
77D MSE 3.4 36.3 - - + +
80D PHE* 5.3 6.0 - - + -
82D ILE* 3.8 21.3 - - + -
272D ILE* 3.6 24.9 - - + -
292D LEU* 3.8 29.4 - - + -
333D LEU* 4.7 1.8 - - + -
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 6.1 1.0 - - - +
34B ILE* 5.6 4.2 - - - +
32D ALA* 5.8 0.2 - - + -
33D PRO* 3.9 21.8 - - + -
36D ALA* 4.0 41.2 - - + +
39D PHE* 4.1 11.9 - - + -
64D VAL 3.0 21.5 + - - +
65D GLN* 3.6 13.0 - - - +
66D GLU 3.2 0.2 - - - -
67D TRP* 1.3 93.8 - - + +
69D ARG* 1.3 69.2 + - - +
70D ALA 3.2 1.1 + - - -
71D GLY 3.9 11.8 + - - +
72D GLY* 4.2 3.7 - - - -
292D LEU* 3.6 33.7 - - + -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 5.8 1.3 - - - +
34B ILE* 4.4 16.4 - - - +
255B ARG* 5.6 3.6 - - - +
277B LEU* 3.5 24.1 - - + +
287B GLN* 3.2 30.5 - - - +
288B TYR 3.6 19.1 + - - +
289B GLU* 3.2 29.7 + - - -
291B ARG* 5.2 2.2 - - - +
36D ALA* 4.7 13.7 + - - +
37D GLY* 4.8 6.5 - - - -
40D ALA* 4.9 6.9 - - - +
65D GLN* 3.0 38.0 + - + +
66D GLU* 3.3 7.2 + - - +
68D LEU* 1.3 91.8 - - - +
70D ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 4.3 16.4 - - - +
287B GLN* 4.8 8.4 - - - +
66D GLU* 2.9 23.5 + - + +
67D TRP* 4.1 4.5 - - - +
69D ARG* 1.3 80.5 - - - +
71D GLY* 1.3 58.2 + - - +
76D ASN* 6.5 0.9 - - + -
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Residues in contact with GLY 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.2 30.8 - - - +
31B GLY* 3.8 2.1 - - - -
32D ALA* 3.3 14.9 - - - +
67D TRP 3.3 0.6 + - - -
68D LEU 4.0 7.0 - - - +
69D ARG 3.8 0.6 - - - -
70D ALA* 1.3 82.8 - - - +
72D GLY* 1.3 61.3 + - - +
73D ASP* 3.4 6.9 + - - +
76D ASN* 5.1 6.7 - - - +
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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