Contacts of the helix formed by residues 55 - 73 (chain D) in PDB entry 5U8T
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 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D VAL* 1.3 82.0 - - - +
56D PRO* 1.3 61.5 - - - +
57D GLN* 3.1 20.6 + - - +
58D GLN* 2.7 49.1 + - - +
59D ASP* 2.9 13.7 + - - +
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Residues in contact with PRO 56 (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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55B THR* 4.1 20.9 - - - +
56B ASP* 5.1 3.4 - - - +
54D VAL 3.2 7.4 - - - +
55D SER* 1.3 83.1 - - - +
57D GLN* 1.3 70.2 + - - +
59D ASP* 3.2 19.4 - - - +
60D PHE* 3.6 7.3 + - - +
90D ARG* 3.2 34.0 + - - +
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Residues in contact with GLN 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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55B THR 3.4 17.7 + - - -
56B ASP* 3.4 38.3 + - + +
58B LYS* 3.8 19.4 - - - +
55D SER* 3.1 16.0 + - - +
56D PRO* 1.3 83.0 - - - +
58D GLN* 1.3 59.0 + - - +
59D ASP 3.1 1.6 - - - -
60D PHE* 3.2 5.2 + - - +
61D SER* 2.4 37.1 + - - +
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Residues in contact with GLN 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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54D VAL 5.2 4.0 - - - +
55D SER* 2.7 37.1 + - - +
57D GLN* 1.3 73.8 - - - +
59D ASP* 1.3 61.2 + - - +
61D SER* 3.4 14.8 + - - -
62D ASP* 2.9 45.9 + - - +
83D LEU* 5.2 1.6 - - + -
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Residues in contact with ASP 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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54D VAL* 4.0 9.8 + - - +
55D SER 2.9 16.1 - - - +
56D PRO* 3.2 10.1 - - - +
58D GLN* 1.3 79.4 - - - +
60D PHE* 1.3 57.5 + - - +
62D ASP* 3.6 1.7 + - - +
63D LEU* 2.9 26.4 + - - +
83D LEU* 3.6 34.7 - - + +
86D ARG* 3.8 6.7 + - - -
87D LEU* 3.5 21.1 - - + +
90D ARG* 2.3 42.0 + - - -
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Residues in contact with PHE 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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18B PHE* 5.4 2.2 - + - -
22B ASN* 4.5 27.1 - - + -
56B ASP* 4.3 24.5 - - + +
56D PRO 3.6 6.9 + - - +
57D GLN* 3.2 9.2 + - - +
59D ASP* 1.3 76.5 - - - +
61D SER* 1.3 62.1 + - - +
63D LEU* 3.4 22.4 - - + -
64D MET* 2.9 57.5 + - + +
87D LEU* 5.6 0.2 - - - -
135D ARG* 6.2 1.6 - - - -
136D LEU* 4.2 21.5 - - + -
139D VAL* 3.6 31.9 - - + -
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Residues in contact with SER 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 GLN* 2.4 30.5 + - - +
58D GLN* 3.4 21.6 + - - -
59D ASP 3.3 0.2 - - - -
60D PHE* 1.3 81.6 - - - +
62D ASP* 1.3 64.2 + - - +
64D MET* 3.7 4.8 + - - +
65D LYS* 2.9 26.4 + - - +
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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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58D GLN* 2.9 28.7 + - - +
59D ASP 3.7 3.1 - - - +
61D SER* 1.3 79.7 - - - +
63D LEU* 1.3 59.7 + - - +
65D LYS* 3.5 27.3 - - + +
66D SER* 2.9 27.2 + - - -
83D LEU* 4.4 17.4 - - + +
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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 ASP 2.9 18.1 + - - +
60D PHE* 3.5 30.1 - - + +
61D SER 3.2 0.2 - - - -
62D ASP* 1.3 76.5 - - - +
64D MET* 1.3 60.4 + - - +
66D SER* 3.4 6.5 + - - -
67D TRP* 2.9 28.5 + - + +
80D PRO* 6.5 0.7 - - + -
84D MET* 4.9 11.4 - - + -
87D LEU* 4.3 20.6 - - + -
136D LEU* 4.3 13.7 - - + -
139D VAL* 3.8 19.3 - - + -
140D ILE* 3.7 31.2 - - + -
143D TYR* 5.6 4.5 - - + -
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Residues in contact with MET 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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18B PHE* 5.1 8.1 - - + -
19B ILE* 3.9 29.8 - - + -
22B ASN* 4.6 6.3 - - + +
60D PHE* 2.9 54.0 + - + +
61D SER* 3.9 4.5 - - - +
63D LEU* 1.3 75.4 - - - +
65D LYS* 1.3 65.4 + - - +
67D TRP* 4.0 15.7 - - + -
68D LYS* 2.8 60.0 + - + +
139D VAL* 4.2 16.4 - - - -
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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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61D SER* 2.9 19.3 + - - +
62D ASP* 3.5 28.5 - - + +
63D LEU 3.3 0.2 - - - -
64D MET* 1.3 75.0 - - - +
66D SER* 1.3 56.5 + - - +
68D LYS* 4.8 4.2 - - - +
69D ASN* 3.0 51.4 + - - +
289D ASP* 4.9 23.9 + - + +
291D VAL 6.1 0.4 - - - -
292D ALA* 5.1 15.4 - - - +
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Residues in contact with SER 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 ASP 2.9 19.1 + - - -
63D LEU* 3.6 8.7 - - - -
64D MET 3.2 0.2 - - - -
65D LYS* 1.3 78.4 - - - +
67D TRP* 1.3 57.1 + - - +
69D ASN* 3.7 3.8 - - - +
70D GLU* 2.8 29.6 + - - +
78D PRO 5.4 0.5 + - - -
80D PRO* 3.8 16.1 - - - +
143D TYR* 3.0 31.5 + - - -
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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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11B PHE* 3.5 39.5 - + - -
15B GLU* 4.0 20.4 - - + -
18B PHE* 6.1 4.3 - + - -
19B ILE* 4.2 11.7 - - + -
63D LEU 2.9 17.8 + - - +
64D MET* 3.1 20.4 + - + +
66D SER* 1.3 74.3 - - - +
68D LYS* 1.3 90.0 + - + +
70D GLU* 2.7 24.4 + - - +
71D ARG* 3.0 24.9 + - + +
138D PHE* 5.4 11.4 - + - -
139D VAL* 3.1 32.1 + - + +
142D SER* 3.1 28.3 + - - -
143D TYR* 3.4 31.2 - - + -
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Residues in contact with LYS 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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11B PHE* 3.4 24.9 - - + -
19B ILE* 3.8 28.8 - - + +
117B TRP* 5.3 5.9 - - - -
175B LEU* 4.8 14.0 - - - +
64D MET* 2.8 48.4 + - + +
65D LYS* 4.2 3.1 - - - +
67D TRP* 1.3 92.5 - - + +
69D ASN* 1.3 68.8 + - - +
70D GLU 3.3 0.5 + - - -
72D CYS* 3.7 13.7 + - - +
293D LEU* 4.6 13.6 - - - +
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Residues in contact with ASN 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* 3.0 37.5 + - - +
66D SER* 3.9 5.1 - - - +
68D LYS* 1.3 79.9 - - - +
70D GLU* 1.3 57.5 + - - +
73D SER* 3.0 31.8 + - - -
77D LEU* 6.3 1.8 - - + -
286D LEU* 3.8 21.3 + - + +
291D VAL 4.6 3.8 + - - -
292D ALA* 4.5 3.5 - - - +
293D LEU* 3.2 48.7 + - + +
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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 SER 2.8 18.1 + - - +
67D TRP* 2.7 13.0 + - - +
69D ASN* 1.3 74.9 - - - +
71D ARG* 1.3 55.4 + - + +
73D SER* 2.2 30.3 + - - -
76D LEU* 3.3 17.7 - - - +
77D LEU* 4.8 11.3 + - - +
143D TYR* 3.4 42.0 + - + +
146D CYS* 4.4 8.1 - - + -
147D ARG* 3.1 31.3 + - - +
150D LYS* 2.3 27.4 + - - +
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Residues in contact with ARG 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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4B PRO* 4.4 11.7 - - - +
6B HIS 3.6 22.0 + - - -
7B LEU* 3.6 17.8 - - - +
8B GLN* 3.9 13.1 + - - +
9B GLN* 3.6 23.2 - - - +
10B THR 3.7 2.8 + - - -
11B PHE* 3.3 33.2 - - + -
15B GLU* 2.7 44.0 + - - -
67D TRP* 3.0 24.1 + - + +
70D GLU* 1.3 78.7 - - + +
72D CYS* 1.3 60.8 + - - +
73D SER 3.3 5.5 + - - +
142D SER* 3.0 28.8 + - - +
146D CYS* 3.9 27.5 - - + +
150D LYS* 3.8 5.2 + - - -
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Residues in contact with CYS 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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9B GLN* 3.9 14.3 + - - +
11B PHE* 4.6 3.5 - - + -
182B ARG* 3.6 43.1 - - - +
68D LYS 3.7 16.6 + - - +
70D GLU 3.3 0.6 - - - -
71D ARG* 1.3 77.0 - - - +
73D SER* 1.3 65.3 + - - +
228D VAL* 3.4 35.2 - - - +
229D PHE 4.7 8.1 - - - -
293D LEU* 4.3 22.9 - - + +
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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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9B GLN* 5.3 5.2 - - - +
69D ASN 3.0 19.2 + - - -
70D GLU* 2.2 29.7 + - - -
71D ARG 3.2 3.0 - - - +
72D CYS* 1.3 81.4 - - - +
74D PRO* 1.3 73.9 - - - +
75D GLU 3.8 14.0 + - - -
77D LEU* 5.5 8.9 + - - -
150D LYS* 2.3 26.9 + - - -
279D TYR* 5.5 1.3 - - - -
286D LEU* 5.9 0.9 - - - -
293D LEU* 4.6 5.6 - - - -
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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