Contacts of the helix formed by residues 53 - 73 (chain D) in PDB entry 3HOU
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 SER 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ASN* 3.7 4.9 + - - -
52D LEU* 1.3 80.5 + - - +
54D GLU* 1.3 58.3 + - - +
55D ALA 2.8 4.0 - - - -
56D ARG* 2.7 7.8 + - - +
57D LEU* 2.6 41.8 + - - +
148D LEU* 3.3 10.9 - - - +
152D SER* 3.6 29.0 + - - -
153D ARG* 4.0 2.4 - - - +
154D PHE* 3.2 42.5 + - - -
160D VAL* 4.3 2.9 - - - +
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Residues in contact with GLU 54 (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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49D ALA 4.6 3.6 - - - +
50D LEU* 3.9 23.4 - - + +
51D ASN* 3.0 48.3 + - - +
52D LEU 2.3 18.2 + - - -
53D SER* 1.3 71.0 + - - +
55D ALA* 1.3 54.3 + - - +
57D LEU* 3.9 5.3 - - - +
58D VAL* 2.9 34.1 + - + +
160D VAL* 4.0 23.3 - - + -
164D ILE* 2.9 31.0 - - + +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 3.8 23.3 - - + -
51D ASN 3.2 14.7 + - - +
52D LEU* 4.2 1.6 - - - -
53D SER 2.8 0.2 - - - -
54D GLU* 1.3 77.0 - - - +
56D ARG* 1.3 64.9 + - - +
57D LEU 3.0 1.8 - - - -
58D VAL* 3.2 1.1 + - - +
59D ILE* 3.0 31.6 + - + +
148D LEU* 3.7 20.6 - - + -
2G PHE* 4.4 17.5 - - + -
77G VAL* 5.9 1.3 - - + -
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER* 2.7 14.5 + - - +
55D ALA* 1.3 78.3 - - - +
57D LEU* 1.3 92.1 + - - +
60D LYS* 3.1 38.1 + - - +
122D GLU* 3.0 40.7 + - - +
126D ILE* 4.7 0.4 - - + -
145D MET* 3.7 19.0 - - + +
148D LEU* 3.3 23.1 - - + +
149D THR* 3.6 15.3 - - - +
152D SER* 3.2 26.7 + - - +
154D PHE 3.3 5.9 + - - -
155D ARG* 3.1 37.5 + - - +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D SER 2.6 20.8 + - - +
54D GLU* 3.9 5.2 - - + +
56D ARG* 1.3 107.8 - - - +
58D VAL* 1.3 61.2 + - + +
60D LYS* 3.2 7.0 + - + +
61D GLU* 2.8 34.4 + - - +
155D ARG 4.8 7.4 - - - +
157D GLN* 3.3 42.4 - - + +
160D VAL* 3.6 33.7 - - + -
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 3.7 19.3 - - + -
54D GLU* 2.9 27.6 + - + +
55D ALA 3.2 5.3 + - - +
57D LEU* 1.3 78.6 - - + +
59D ILE* 1.3 65.8 + - - +
61D GLU* 3.8 7.5 - - - +
62D ALA* 3.2 18.5 + - - +
4G ILE* 4.1 13.0 - - + -
49G LEU* 4.0 15.0 - - + -
77G VAL* 3.9 21.8 - - + -
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Residues in contact with ILE 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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55D ALA* 3.0 20.0 + - + +
56D ARG 4.2 0.2 - - - +
58D VAL* 1.3 76.1 - - - +
60D LYS* 1.3 65.6 + - - +
62D ALA* 3.1 5.2 + - - +
63D LEU* 3.0 35.6 + - + +
141D LEU* 4.0 24.2 - - + -
144D THR* 4.3 8.7 - - + -
145D MET* 3.5 33.9 - - + -
148D LEU* 4.1 12.3 - - + -
2G PHE* 5.4 0.7 - - + -
46G LEU* 4.9 1.3 - - + -
47G CYS* 4.3 16.2 - - + -
77G VAL* 4.0 32.8 - - + -
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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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56D ARG* 3.1 27.9 + - - +
57D LEU* 3.8 5.5 - - + +
59D ILE* 1.3 81.5 - - - +
61D GLU* 1.3 64.5 + - - +
63D LEU* 3.3 3.8 + - - +
64D VAL* 3.0 32.3 + - + +
122D GLU* 2.7 40.2 + - - +
126D ILE* 3.9 18.4 - - + -
129D LEU* 3.8 20.4 - - + +
145D MET* 4.5 6.5 - - + -
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Residues in contact with GLU 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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57D LEU 2.8 21.8 + - - +
58D VAL* 3.8 7.2 - - - +
60D LYS* 1.3 70.9 - - - +
62D ALA* 1.3 65.3 + - - +
64D VAL* 3.0 23.4 + - - +
65D GLU* 3.1 32.1 + - - +
157D GLN* 5.4 3.6 - - - +
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Residues in contact with ALA 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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58D VAL 3.2 9.4 + - - +
59D ILE 3.1 8.1 + - - +
61D GLU* 1.3 77.8 - - - +
63D LEU* 1.3 64.5 + - - +
64D VAL 2.9 5.7 + - - -
65D GLU* 3.2 7.7 + - - +
66D ARG* 2.9 24.0 + - - +
47G CYS* 4.3 6.7 - - - -
48G VAL 4.5 1.8 - - - +
49G LEU* 4.1 33.9 - - + -
50G ASP* 4.4 6.7 - - - +
51G TYR* 5.7 3.0 + - - +
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Residues in contact with LEU 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 ILE* 3.0 26.8 + - + +
60D LYS* 3.8 1.1 - - - +
62D ALA* 1.3 75.7 - - - +
64D VAL* 1.3 57.7 + - - +
66D ARG* 3.8 28.9 - - - +
67D ARG 3.2 3.6 + - - -
129D LEU* 3.1 25.5 - - + +
130D LEU* 3.6 31.2 - - + -
133D THR* 3.1 37.0 - - - +
134D THR* 3.8 9.9 - - - +
141D LEU* 4.3 11.0 - - + -
145D MET* 5.5 0.9 - - + -
47G CYS* 3.6 26.5 - - - -
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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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60D LYS* 3.0 31.3 + - + +
61D GLU* 3.0 12.0 + - - +
62D ALA 2.9 1.8 + - - -
63D LEU* 1.3 74.7 - - - +
65D GLU* 1.3 57.4 + - - +
66D ARG 2.8 13.3 + - - -
67D ARG* 2.9 21.3 + - - +
68D ARG* 2.9 43.3 + - + +
129D LEU* 3.6 21.5 - - + -
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Residues in contact with GLU 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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61D GLU* 3.1 38.2 + - - +
62D ALA* 4.0 7.4 - - - +
64D VAL* 1.3 80.7 - - - +
66D ARG* 1.3 61.0 + - - +
68D ARG* 3.4 33.5 + - - +
69D ALA* 3.2 20.1 + - - +
72D ARG* 3.5 19.0 + - - +
50G ASP* 6.6 0.2 - - - -
51G TYR* 5.4 2.6 - - + +
52G ASP* 4.2 8.4 - - - +
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Residues in contact with ARG 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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62D ALA* 2.9 16.0 + - - +
63D LEU* 3.6 26.3 - - - +
64D VAL 2.8 1.0 + - - -
65D GLU* 1.3 76.0 - - - +
67D ARG* 1.3 54.5 + - - +
68D ARG 2.6 4.5 + - - -
69D ALA* 2.9 3.6 + - - +
70D PHE* 2.6 61.2 + - + +
133D THR* 2.9 39.8 + - + -
134D THR* 4.5 0.8 + - - +
31G LEU* 3.5 18.9 - - - +
35G GLU* 2.4 42.4 + - - -
48G VAL* 2.9 25.5 + - - +
51G TYR* 3.9 27.6 - - + +
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Residues in contact with ARG 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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63D LEU 3.2 3.1 + - - +
64D VAL* 2.9 14.2 + - - +
66D ARG* 1.3 78.4 - - - +
68D ARG* 1.3 64.2 + - - +
70D PHE* 3.4 8.2 - - + +
71D LYS* 3.3 52.2 - - - +
125D SER 5.7 0.4 + - - -
128D VAL* 4.9 3.2 - - - +
129D LEU* 3.6 28.6 - - + +
132D GLN* 3.5 33.8 + - + +
133D THR* 3.1 24.7 - - + +
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Residues in contact with ARG 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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64D VAL* 2.9 28.9 + - + +
65D GLU* 3.4 42.2 + - - +
66D ARG 2.6 5.3 + - - -
67D ARG* 1.3 73.4 - - + +
69D ALA* 1.3 54.3 + - - +
70D PHE 2.9 3.6 - - - -
71D LYS* 2.8 26.2 + - - +
72D ARG* 3.0 30.2 + - - +
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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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65D GLU 3.2 8.6 + - - +
66D ARG 2.9 5.1 + - - +
68D ARG* 1.3 71.0 - - - +
70D PHE* 1.3 57.1 + - - +
71D LYS 2.8 11.0 + - - -
72D ARG* 3.3 29.8 + - + +
73D SER* 3.3 18.7 + - - -
24G GLN* 5.3 1.9 + - - -
51G TYR* 4.7 15.4 - - + -
52G ASP* 3.0 28.5 - - - +
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Residues in contact with PHE 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 ARG* 2.6 44.2 + - + +
67D ARG* 3.4 13.0 - - + +
68D ARG 2.9 0.4 - - - -
69D ALA* 1.3 69.4 - - - +
71D LYS* 1.3 62.6 - - + +
73D SER* 4.4 6.1 - - - -
74D GLN* 2.8 20.3 + - - +
132D GLN 3.9 23.1 - - - -
133D THR* 4.4 12.8 - - + -
24G GLN* 5.7 4.9 - - - +
28G THR* 5.9 2.5 - - - -
31G LEU* 5.0 5.4 - - + -
51G TYR* 3.5 38.6 - + - -
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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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67D ARG* 3.3 43.5 - - + +
68D ARG* 2.8 9.8 + - - +
69D ALA 2.8 0.4 - - - -
70D PHE* 1.3 92.8 - - - +
72D ARG* 1.3 63.2 + - - +
73D SER 3.0 2.0 - - - -
74D GLN* 3.2 35.2 + - + +
75D LYS* 3.7 11.8 + - - +
132D GLN* 3.7 16.2 - - - +
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Residues in contact with ARG 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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65D GLU* 3.5 26.9 + - - +
68D ARG* 3.0 26.7 + - - +
69D ALA* 3.3 20.8 + - - +
71D LYS* 1.3 78.2 - - - +
73D SER* 1.3 58.1 + - - +
75D LYS* 3.5 21.5 - - - +
52G ASP* 2.7 40.1 + - - -
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Residues in contact with SER 73 (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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69D ALA 3.3 15.1 + - - -
70D PHE* 4.4 5.0 - - - -
72D ARG* 1.3 79.3 - - - +
74D GLN* 1.3 62.2 + - - +
75D LYS* 3.1 3.1 + - - -
76D LYS 3.7 19.4 + - - +
21G ARG* 3.4 30.1 - - - -
24G GLN* 3.8 21.3 + - - +
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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