Contacts of the helix formed by residues 56 - 72 (chain D) in PDB entry 1HYH
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 GLU 56 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA 3.3 7.7 + - - +
55D ASN* 1.3 73.6 + - - +
57D ALA* 1.3 56.8 + - - +
59D VAL* 3.4 6.5 - - - +
60D LYS* 3.0 35.3 + - + +
81D ILE* 3.7 19.8 - - - +
82D ASN* 2.9 27.6 + - - +
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Residues in contact with ALA 57 (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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244B GLY* 3.7 20.7 - - - +
55D ASN* 3.1 9.8 + - - +
56D GLU* 1.3 75.2 - - - +
58D LYS* 1.3 64.6 + - - +
60D LYS* 3.5 5.5 + - - +
61D ALA* 3.0 25.5 + - - +
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Residues in contact with LYS 58 (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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244B GLY 3.6 10.7 + - - +
245B LYS* 3.6 26.9 - - + -
247B TYR* 4.8 10.9 + - - -
29D LEU 2.8 27.2 + - - +
30D GLY* 4.4 7.8 + - - -
34D ALA* 4.3 9.7 - - - +
53D ASP* 5.0 2.0 - - - +
55D ASN* 3.3 28.0 + - + +
57D ALA* 1.3 76.3 - - - +
59D VAL* 1.3 63.9 + - - +
61D ALA* 3.1 5.2 + - - +
62D ASP* 2.6 49.1 + - - +
330D NAD 4.5 9.9 - - - +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 4.1 9.9 - - + -
51D PHE* 3.6 35.9 - - + +
53D ASP* 3.7 24.7 - - + +
55D ASN 3.2 8.0 + - - +
56D GLU 3.4 11.4 - - - +
58D LYS* 1.3 79.3 - - - +
60D LYS* 1.3 59.9 + - - +
62D ASP* 3.6 6.6 + - - +
63D GLN* 3.0 27.5 + - - +
81D ILE* 3.8 18.2 - - + +
82D ASN* 3.6 26.5 - - - +
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Residues in contact with LYS 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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240B THR* 5.3 6.7 - - + -
56D GLU* 3.0 24.6 + - + +
57D ALA* 3.7 6.7 - - - +
59D VAL* 1.3 75.5 - - - +
61D ALA* 1.3 64.9 + - - +
63D GLN* 3.1 25.5 + - - +
64D ILE* 3.1 49.3 + - + +
67D GLN* 5.7 0.8 - - - +
81D ILE* 3.8 17.7 - - + +
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Residues in contact with ALA 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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240B THR* 4.4 2.9 - - - +
241B VAL* 3.6 37.3 - - - +
244B GLY* 3.8 11.7 - - - -
245B LYS* 3.9 12.6 - - + -
57D ALA 3.0 17.6 + - - +
58D LYS 3.1 5.1 + - - +
60D LYS* 1.3 73.6 - - - +
62D ASP* 1.3 60.4 + - - +
64D ILE* 3.3 5.3 + - - +
65D ASP* 2.9 29.4 + - - +
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Residues in contact with ASP 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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245B LYS* 2.7 38.4 + - - +
247B TYR* 5.2 0.3 + - - -
250B TYR* 3.6 11.7 + - - -
29D LEU* 3.9 18.5 - - + +
34D ALA* 4.4 3.3 - - - +
51D PHE* 4.8 6.5 - - + -
58D LYS* 2.6 41.1 + - - +
59D VAL* 3.8 8.7 - - - +
61D ALA* 1.3 75.6 - - - +
63D GLN* 1.3 66.6 + - - +
65D ASP* 3.2 1.4 + - - +
66D PHE* 2.8 39.5 + - + -
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Residues in contact with GLN 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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51D PHE* 4.8 2.2 - - - -
59D VAL 3.0 19.7 + - - +
60D LYS* 3.1 36.6 + - - +
61D ALA 3.3 0.2 - - - -
62D ASP* 1.3 76.1 - - - +
64D ILE* 1.3 55.9 + - - +
66D PHE* 3.4 1.9 + - - +
67D GLN* 2.9 55.2 + - - +
79D ILE* 2.8 51.7 + - + +
80D VAL* 4.0 7.5 - - - +
81D ILE* 3.9 17.6 - - + +
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Residues in contact with ILE 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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177B ARG* 3.9 28.9 - - - +
233B GLU* 5.1 8.7 - - - +
237B GLY* 4.3 4.0 - - - +
240B THR* 4.1 26.7 - - + -
241B VAL* 3.5 20.6 - - + -
60D LYS* 3.1 40.8 + - + +
61D ALA* 3.8 3.4 - - - +
62D ASP 3.3 0.2 - - - -
63D GLN* 1.3 73.4 - - - +
65D ASP* 1.3 59.5 - - - +
67D GLN* 3.2 19.4 + - - +
68D ASP* 2.9 32.1 + - - +
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 5.2 2.4 + - - -
241B VAL* 3.9 13.3 - - + +
245B LYS* 2.8 28.5 + - - +
248B THR* 4.2 6.4 - - - -
249B SER 2.8 23.8 + - - -
250B TYR* 3.2 16.0 + - + -
251B GLY* 3.2 26.3 + - - -
252B VAL 5.1 0.2 + - - -
61D ALA 2.9 15.9 + - - +
62D ASP 3.2 4.9 + - - +
64D ILE* 1.3 75.8 - - - +
66D PHE* 1.3 62.4 + - - +
68D ASP* 3.3 12.6 + - - +
69D ALA* 3.2 15.8 + - - +
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Residues in contact with PHE 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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250B TYR* 3.5 51.1 - + + -
29D LEU* 5.4 1.6 - - + -
34D ALA* 4.1 2.0 - - - -
37D ALA* 3.9 17.5 - - + -
38D HIS* 3.6 39.7 - + - -
41D ILE* 3.8 24.0 - - + -
51D PHE* 3.9 22.0 - + - -
62D ASP* 2.8 28.5 + - + +
65D ASP* 1.3 74.6 - - - +
67D GLN* 1.3 64.1 + - - +
69D ALA* 3.2 16.1 + - + +
70D MET* 3.3 20.7 + - + +
79D ILE* 3.5 18.2 - - + -
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Residues in contact with GLN 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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173B ALA 5.0 0.5 - - - +
177B ARG* 3.5 25.7 - - + +
181B GLU* 3.5 25.0 + - - +
187B PRO* 4.9 3.3 - - - +
60D LYS* 5.7 0.8 - - - +
63D GLN* 2.9 53.8 + - + +
64D ILE* 3.2 21.3 + - - +
66D PHE* 1.3 77.4 - - - +
68D ASP* 1.3 60.5 + - - +
70D MET* 3.4 25.0 + - + +
71D ALA 4.4 1.9 + - - -
79D ILE* 4.2 15.7 + - + +
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Residues in contact with ASP 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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170B LEU* 4.5 3.4 - - + -
173B ALA* 3.2 30.5 - - - +
174B ARG* 3.0 48.5 + - + +
177B ARG* 2.7 32.9 + - - +
237B GLY 5.1 0.2 - - - +
241B VAL* 4.7 2.8 - - - +
251B GLY* 4.2 14.4 - - - +
64D ILE* 2.9 23.4 + - - +
65D ASP* 3.4 13.6 - - - +
66D PHE 3.2 0.4 - - - -
67D GLN* 1.3 77.5 - - - +
69D ALA* 1.3 59.9 + - - +
70D MET 3.4 0.2 - - - -
71D ALA 4.1 2.4 + - - -
72D ASN* 4.8 1.4 + - - -
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Residues in contact with ALA 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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250B TYR* 3.7 13.9 - - + +
251B GLY* 4.0 6.0 - - - -
254B THR* 3.6 28.5 - - + +
65D ASP 3.2 9.8 + - - +
66D PHE* 3.2 15.7 + - + +
68D ASP* 1.3 76.3 - - - +
70D MET* 1.3 63.0 + - - +
71D ALA 3.3 0.4 - - - -
72D ASN* 2.9 17.7 + - - +
73D LEU* 3.3 21.0 + - + +
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Residues in contact with MET 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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186B ASP* 5.8 0.2 - - - +
187B PRO* 3.8 19.1 - - + -
188B ARG* 3.7 10.2 - - - +
41D ILE* 3.8 29.8 - - + -
66D PHE 3.3 22.6 + - - +
67D GLN* 3.6 16.6 - - + +
68D ASP 3.4 0.8 - - - -
69D ALA* 1.3 74.2 - - - +
71D ALA* 1.3 62.4 + - - +
72D ASN 3.2 1.0 + - - -
73D LEU* 3.3 22.7 + - + +
75D ALA 3.9 14.9 - - - +
76D HIS* 4.1 11.0 - - + +
77D GLY* 3.6 44.0 - - - +
79D ILE* 4.8 10.3 - - + -
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Residues in contact with ALA 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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173B ALA* 4.0 20.2 - - + +
176B GLN* 3.2 44.0 + - + +
187B PRO* 4.3 10.5 - - + +
188B ARG* 3.8 20.8 - - - +
258B ARG* 4.1 8.5 + - - -
67D GLN 4.4 1.6 + - - -
68D ASP 4.1 2.4 + - - -
69D ALA 3.0 2.2 + - - -
70D MET* 1.3 76.6 - - - +
72D ASN* 1.3 62.4 + - - +
73D LEU 3.5 0.9 + - - +
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Residues in contact with ASN 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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169B LEU* 3.9 17.3 + - - +
173B ALA* 3.8 21.6 - - - +
176B GLN* 5.0 2.4 - - - +
251B GLY 4.9 0.6 + - - -
254B THR* 3.5 28.1 - - + +
255B SER* 2.8 27.8 + - - -
258B ARG* 2.8 57.3 + - - +
68D ASP 4.8 1.4 + - - -
69D ALA* 2.9 5.7 + - - +
71D ALA* 1.3 77.9 - - - +
73D LEU* 1.3 58.3 + - - +
74D 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
------------------------------------------------------------
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