Contacts of the helix formed by residues 63 - 77 (chain D) in PDB entry 2IYL
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 ASP 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.4 27.9 - - - +
62D LYS* 1.3 76.8 - - - +
64D LEU* 1.3 56.0 + - - +
65D LYS* 3.6 6.4 + - - +
66D GLU* 3.1 35.0 + - + +
67D ALA* 2.9 26.8 + - - +
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Residues in contact with LEU 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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24D TRP* 3.7 11.9 - - + -
25D GLY* 4.9 11.2 - - - +
26D GLY 5.1 3.8 - - - +
28D LEU* 4.3 28.7 - - + +
31D VAL* 4.2 32.3 - - + -
32D LEU* 5.8 1.8 - - + -
56D VAL* 4.5 22.0 - - + +
61D ARG 4.0 17.0 - - - +
62D LYS* 3.3 12.1 + - - +
63D ASP* 1.3 70.2 + - - +
65D LYS* 1.3 60.0 + - - +
67D ALA* 3.6 8.0 - - - +
68D VAL* 2.8 33.7 + - + +
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Residues in contact with LYS 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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24D TRP* 3.4 63.7 - - + +
63D ASP* 3.4 5.7 + - - +
64D LEU* 1.3 75.0 - - - +
66D GLU* 1.3 61.8 + - - +
68D VAL* 3.4 2.1 + - - +
69D LYS* 2.9 54.4 + - + +
299D GLU* 4.0 22.8 + - - +
302D LEU* 4.7 16.0 + - + -
303D GLU* 6.2 1.0 - - - +
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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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63D ASP* 3.1 32.1 + - + +
65D LYS* 1.3 79.7 - - - +
67D ALA* 1.3 62.3 + - - +
69D LYS* 3.4 23.9 + - - +
70D GLU* 3.1 45.3 + - - +
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Residues in contact with ALA 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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56D VAL* 5.0 10.3 - - + +
59D SER* 5.5 7.9 - - - +
61D ARG* 4.5 17.5 - - + -
63D ASP 2.9 18.9 + - - +
64D LEU* 3.8 9.6 - - + +
65D LYS 3.2 0.2 - - - -
66D GLU* 1.3 75.7 - - - +
68D VAL* 1.3 61.1 + - - +
70D GLU* 3.5 10.7 + - - +
71D LYS* 3.0 40.5 + - - +
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Residues in contact with VAL 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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24D TRP* 4.1 12.3 - - + -
31D VAL* 5.9 0.7 - - + -
35D LEU* 3.5 43.5 - - + -
52D ILE* 4.9 3.1 - - + +
56D VAL* 3.8 23.8 - - + -
64D LEU* 2.8 25.5 + - + +
65D LYS 3.8 3.4 - - - +
67D ALA* 1.3 74.5 - - - +
69D LYS* 1.3 65.4 + - - +
71D LYS* 3.1 4.7 + - - +
72D LEU* 3.0 44.0 + - + +
302D LEU* 4.1 10.5 - - + -
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Residues in contact with LYS 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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65D LYS* 2.9 49.0 + - - +
66D GLU* 3.7 24.7 + - - +
68D VAL* 1.3 74.8 - - - +
70D GLU* 1.3 56.0 + - + +
72D LEU* 3.3 0.5 + - - +
73D VAL* 2.7 42.9 + - + +
295D GLU 6.0 0.4 - - - +
298D VAL* 3.7 26.9 - - + -
299D GLU* 3.2 29.5 + - + +
302D LEU* 4.0 8.5 - - + -
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Residues in contact with GLU 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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66D GLU* 3.1 41.9 + - - +
67D ALA* 3.8 10.6 - - - +
68D VAL 3.3 0.2 - - - -
69D LYS* 1.3 76.6 - - + +
71D LYS* 1.3 67.2 + - - +
73D VAL* 4.1 3.9 - - - +
74D GLY* 2.8 27.4 + - - -
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Residues in contact with LYS 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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52D ILE* 4.7 13.2 - - + -
55D GLU* 3.1 39.3 + - + +
56D VAL* 4.3 16.4 - - + +
59D SER* 3.5 23.9 + - - -
67D ALA* 3.0 25.1 - - - +
68D VAL* 3.1 5.8 + - - +
70D GLU* 1.3 87.5 - - + +
72D LEU* 1.3 56.3 - - - +
74D GLY* 3.6 1.7 + - - -
75D MET* 3.1 31.9 + - - +
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Residues in contact with LEU 72 (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 LEU* 4.1 15.0 - - + -
44D VAL* 5.2 0.4 - - + -
52D ILE* 3.7 27.4 - - + -
68D VAL* 3.0 37.9 + - + +
69D LYS 3.8 0.9 - - - +
71D LYS* 1.3 74.0 - - - +
73D VAL* 1.3 67.1 + - - +
75D MET* 3.3 18.8 + - - +
76D LEU* 3.4 14.2 + - - +
267D ILE* 3.3 27.3 - - + +
298D VAL* 3.7 26.0 - - + -
301D LEU* 4.1 11.0 - - + -
302D LEU* 4.0 17.7 - - + -
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D LYS* 2.7 29.2 + - + +
70D GLU* 4.1 3.8 - - - +
72D LEU* 1.3 70.2 - - - +
74D GLY* 1.3 65.3 + - - +
76D LEU* 3.0 18.9 + - - +
77D GLU* 3.2 40.4 + - + +
294D PRO* 4.1 8.7 - - + +
295D GLU* 3.9 33.9 - - + +
298D VAL* 3.8 23.5 - - + +
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Residues in contact with GLY 74 (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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70D GLU 2.8 23.8 + - - -
71D LYS* 3.7 2.7 - - - -
73D VAL* 1.3 76.4 - - - +
75D MET* 1.3 58.0 + - - +
76D LEU 3.5 0.5 + - - -
77D GLU* 3.5 20.7 + - - +
78D PRO* 4.5 1.7 - - - +
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Residues in contact with MET 75 (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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48D ALA* 3.7 7.0 - - + -
51D GLU* 5.4 0.9 - - + -
52D ILE* 3.4 28.0 - - + -
71D LYS* 3.1 15.7 + - - +
72D LEU* 3.3 15.9 - - - +
73D VAL 3.2 0.2 - - - -
74D GLY* 1.3 74.8 - - - +
76D LEU* 1.3 57.6 + - + +
77D GLU 3.5 0.4 - - - -
78D PRO* 4.7 2.3 - - - +
267D ILE* 3.2 26.7 - - + +
270D VAL* 3.1 25.1 - - - +
271D ARG* 2.8 59.7 + - + +
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Residues in contact with LEU 76 (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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72D LEU 3.4 15.5 + - - +
73D VAL* 3.0 7.2 + - - +
75D MET* 1.3 75.3 - - - +
77D GLU* 1.3 60.4 + - - +
78D PRO* 3.2 14.7 - - - +
266D LEU* 3.8 36.1 - - + +
267D ILE* 4.3 12.6 - - + +
270D VAL* 3.8 18.4 - - + +
276D PRO* 4.0 12.8 - - - +
277D ILE* 4.6 1.6 + - + -
292D PHE* 4.1 21.7 - - + -
294D PRO* 4.3 18.1 - - + +
297D PHE* 3.6 30.7 - - + -
298D VAL* 4.2 10.3 - - + -
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Residues in contact with GLU 77 (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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73D VAL* 3.2 37.1 + - - +
74D GLY* 3.5 11.8 + - - +
76D LEU* 1.3 82.4 - - - +
78D PRO* 1.3 63.7 - - - +
79D ASP 3.1 14.2 + - - +
94D LYS* 5.5 7.5 + - - -
276D PRO* 5.4 2.7 - - + -
294D PRO* 3.7 25.8 - - + +
295D GLU* 4.6 6.4 - - - +
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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