Contacts of the helix formed by residues 59 - 71 (chain D) in PDB entry 5XAC
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 ASN 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D HIS 4.2 3.9 - - - +
58D VAL* 1.3 81.3 - - - +
60D MET* 1.3 66.2 + - - +
61D SER* 3.2 9.2 + - - +
62D GLU* 3.0 30.0 + - - +
63D LEU* 3.3 9.9 + - - +
91D VAL 3.6 11.4 - - - +
92D SER* 3.6 17.8 + - - +
93D THR 3.4 8.7 - - - +
94D PRO* 3.3 23.2 - - - +
95D ILE* 4.5 3.9 - - - +
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Residues in contact with MET 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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59D ASN* 1.3 73.3 - - - +
61D SER* 1.3 57.9 + - - +
63D LEU* 3.1 7.2 + - - +
64D ILE* 2.8 42.2 + - + +
81D LEU* 4.2 33.7 - - + +
83D VAL* 4.6 7.6 - - + -
89D VAL* 3.7 29.2 - - + +
90D SER 4.1 0.2 - - - +
91D VAL* 3.5 18.4 + - - +
93D THR 2.9 17.2 + - - +
95D ILE* 3.7 26.4 - - + +
98D VAL* 3.9 12.8 - - + -
111D MET* 3.8 20.6 - - + -
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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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59D ASN* 3.8 12.5 + - - +
60D MET* 1.3 76.4 - - - +
62D GLU* 1.3 65.2 + - - +
64D ILE* 3.4 8.1 + - - +
65D LYS* 2.9 28.9 + - - +
91D VAL* 3.0 37.1 + - - -
92D SER* 5.4 0.7 - - - -
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Residues in contact with GLU 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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57D HIS* 5.0 2.4 - - - +
58D VAL* 3.3 33.7 - - + +
59D ASN* 3.0 39.4 + - - +
61D SER* 1.3 85.8 + - - +
63D LEU* 1.3 57.6 + - - +
65D LYS* 3.4 8.3 + - - +
66D ILE* 3.0 38.5 + - + +
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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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33D VAL* 4.6 5.2 - - + -
35D ILE* 4.1 21.5 - - + -
52D PHE* 5.8 1.8 - - + -
54D VAL* 4.1 30.7 - - + -
58D VAL* 5.2 1.6 - - + +
59D ASN 3.3 8.0 + - - +
60D MET* 3.1 11.0 + - - +
62D GLU* 1.3 77.2 - - - +
64D ILE* 1.3 65.1 + - - +
66D ILE* 3.2 13.8 + - + +
67D ILE* 3.1 30.6 + - + +
81D LEU* 4.0 10.1 - - + -
95D ILE* 4.1 13.2 - - + -
111D MET* 3.7 38.4 - - + -
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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
----------------------------------------------------------
60D MET* 2.8 38.7 + - + +
61D SER* 3.6 6.3 - - - +
63D LEU* 1.3 72.9 - - - +
65D LYS* 1.3 57.8 + - - +
67D ILE* 3.3 2.3 + - - +
68D ARG* 2.8 53.5 + - - +
79D PHE* 3.9 19.0 - - + +
81D LEU* 3.9 31.4 - - + +
89D VAL 5.9 0.7 - - - +
91D VAL* 3.7 29.6 - - + -
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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 18.3 + - - +
62D GLU* 3.7 8.1 - - - +
64D ILE* 1.3 77.2 - - - +
66D ILE* 1.3 71.0 + - + +
68D ARG* 3.4 9.5 + - + +
69D ARG* 3.0 72.1 + - + +
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Residues in contact with ILE 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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52D PHE* 5.8 3.8 - - + -
54D VAL* 6.0 4.7 - - + -
55D PRO* 6.2 3.4 - - + -
58D VAL* 6.3 3.4 - - + -
62D GLU* 3.0 28.2 + - + +
63D LEU* 3.2 14.8 + - + +
65D LYS* 1.3 86.9 - - + +
67D ILE* 1.3 72.1 + - + +
69D ARG* 3.3 7.5 + - - +
70D ARG* 3.1 31.8 + - + +
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Residues in contact with ILE 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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35D ILE* 3.9 34.8 - - + -
47D LEU* 4.1 18.8 - - + -
52D PHE* 4.0 26.9 - - + -
63D LEU* 3.1 23.1 + - + +
64D ILE 4.0 2.5 - - - +
66D ILE* 1.3 80.4 - - + +
68D ARG* 1.3 65.2 + - - +
70D ARG* 3.3 11.8 + - - +
71D LEU* 3.0 24.4 + - + +
79D PHE* 3.5 27.8 - - + -
81D LEU* 4.8 4.3 - - + -
113D TYR* 4.8 7.4 - - + -
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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
----------------------------------------------------------
64D ILE* 2.8 38.9 + - - +
65D LYS* 3.7 9.4 - - - +
67D ILE* 1.3 76.5 - - - +
69D ARG* 1.3 58.6 + - + +
71D LEU* 3.3 3.1 + - - +
72D GLN 3.1 6.4 + - - -
73D LEU* 3.1 48.4 + - + +
74D ASN 2.5 33.9 + - - -
75D ALA* 3.8 10.1 + - - +
77D GLN 2.8 25.2 + - - -
78D ALA* 4.4 0.4 - - - +
79D PHE* 3.5 41.4 + - + +
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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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88B MET* 3.2 17.8 - - + +
89B VAL 5.0 1.2 + - - -
90B SER* 3.6 39.8 + - - +
91B VAL* 4.5 4.6 - - - +
92B SER* 5.7 1.0 + - - -
65D LYS* 3.0 61.8 + - + +
66D ILE* 3.7 6.1 - - - +
67D ILE 3.2 0.2 - - - -
68D ARG* 1.3 76.6 - - + +
70D ARG* 1.3 65.7 + - - +
72D GLN* 3.0 14.8 + - - +
73D LEU 5.9 0.7 - - - -
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Residues in contact with ARG 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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80B PHE* 3.3 12.1 - - - -
88B MET* 3.2 28.3 - - - +
117B GLU* 2.9 43.2 + - + +
118B THR 3.6 9.5 + - - -
47D LEU* 4.1 15.0 - - + +
49D LYS* 3.5 20.8 - - - +
52D PHE* 3.9 31.9 - - - -
66D ILE* 3.1 23.1 + - + +
67D ILE* 3.6 20.0 - - - +
69D ARG* 1.3 75.7 - - - +
71D LEU* 1.3 58.5 + - - +
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Residues in contact with LEU 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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79B PHE 5.6 0.7 - - - +
80B PHE* 4.1 8.6 - - + -
44D LEU* 4.8 4.5 - - + -
45D PRO* 4.0 40.9 - - + +
47D LEU* 3.7 27.6 - - + -
67D ILE* 3.0 20.2 + - + +
68D ARG 3.7 0.4 - - - +
69D ARG 3.2 0.2 - - - -
70D ARG* 1.3 74.8 - - - +
72D GLN* 1.3 70.0 + - - +
73D LEU* 3.3 27.1 + - + +
79D PHE* 3.5 36.3 - - + -
113D TYR* 4.1 13.9 - - + +
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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