Contacts of the helix formed by residues 58 - 73 (chain D) in PDB entry 1RFU
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 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D LEU* 1.3 75.9 - - - +
59D SER* 1.3 59.1 + - - +
60D ASP* 2.8 25.7 + - - +
61D GLU* 2.7 51.3 + - - +
62D LEU* 3.0 9.9 + - - +
87D ASP* 3.4 15.5 - - - +
90D PHE* 4.2 4.9 - - - -
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Residues in contact with SER 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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58D ASN* 1.3 73.4 - - - +
60D ASP* 1.3 62.0 + - - +
62D LEU* 3.4 2.9 + - - +
63D GLN* 2.9 24.1 + - - +
87D ASP* 4.2 2.0 + - - -
89D SER* 2.8 37.7 + - - -
90D PHE* 4.4 9.4 - - - +
93D MET* 3.2 28.9 - - - +
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Residues in contact with ASP 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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58D ASN* 2.8 19.9 + - - +
59D SER* 1.3 76.1 - - - +
61D GLU* 1.3 60.7 + - + +
63D GLN* 3.1 8.1 + - - +
64D GLU* 2.9 30.9 + - - +
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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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56D VAL 2.9 26.2 - - - +
57D LEU* 3.0 28.4 - - + -
58D ASN* 2.7 37.7 + - - +
60D ASP* 1.3 72.6 - - + +
62D LEU* 1.3 61.4 + - - +
64D GLU* 3.4 19.1 - - - +
65D LEU* 3.3 20.3 - - - +
55G GLN* 4.1 22.7 - - - +
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Residues in contact with LEU 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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10D ILE* 4.9 6.1 - - + -
38D VAL* 3.9 33.0 - - + -
57D LEU* 4.4 1.0 - - - +
58D ASN 3.0 5.7 + - - -
59D SER* 3.8 7.9 - - - +
61D GLU* 1.3 76.5 - - - +
63D GLN* 1.3 65.4 + - - +
65D LEU* 3.3 8.6 + - + +
66D TYR* 2.9 22.9 + - + +
90D PHE* 3.3 39.3 - - + +
93D MET* 4.0 18.8 - - + -
94D VAL* 3.8 22.7 - - + -
97D ILE* 4.1 19.7 - - + -
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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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59D SER 2.9 14.3 + - - +
60D ASP* 3.1 12.3 + - - +
62D LEU* 1.3 74.0 - - - +
64D GLU* 1.3 56.2 + - - +
66D TYR* 3.1 17.0 + - - +
67D ASP* 2.5 73.7 + - - +
93D MET* 2.5 33.5 - - + +
97D ILE* 6.2 0.2 - - - +
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Residues in contact with GLU 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 ASP 2.9 14.0 + - - +
61D GLU* 3.4 14.0 - - - +
63D GLN* 1.3 75.7 - - - +
65D LEU* 1.3 53.8 + - - +
67D ASP* 3.2 7.1 + - - +
68D GLY 2.7 30.5 + - - -
53G LYS* 3.4 29.5 - - + +
54G GLY 3.4 19.7 - - - +
55G GLN* 2.8 27.4 - - - +
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Residues in contact with LEU 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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38D VAL* 3.9 29.8 - - + -
57D LEU* 4.0 6.1 - - + -
61D GLU 3.3 15.9 - - - +
62D LEU* 3.3 9.1 + - + +
63D GLN 3.2 0.6 - - - -
64D GLU* 1.3 79.5 - - - +
66D TYR* 1.3 63.6 + - - +
68D GLY* 2.9 11.8 + - - -
69D LEU* 2.9 19.7 + - + +
15G VAL* 4.4 12.6 - - + -
42G GLN* 3.7 36.3 - - + +
43G PHE 4.1 13.9 - - - -
44G SER* 3.7 6.8 - - - +
53G LYS 4.8 1.1 - - - -
54G GLY* 3.8 15.3 - - - -
55G GLN* 3.8 16.2 - - - +
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Residues in contact with TYR 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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8D LEU* 5.2 7.2 - - + -
62D LEU* 2.9 19.1 + - + +
63D GLN* 3.7 17.3 - - - +
65D LEU* 1.3 75.3 - - - +
67D ASP* 1.3 54.1 + - - +
69D LEU* 3.2 17.5 + - + +
70D LYS* 2.6 42.8 + - + +
75D ASN* 3.4 26.0 + - + -
77D TYR* 5.2 1.3 - + - -
97D ILE* 3.6 50.5 + - + +
100D GLU* 3.3 32.6 + - - -
101D LEU* 3.2 31.0 - - + +
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Residues in contact with ASP 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 GLN* 2.5 59.9 + - - +
64D GLU* 3.4 7.0 - - - +
66D TYR* 1.3 73.3 - - - +
68D GLY* 1.3 54.8 + - - +
70D LYS* 3.0 9.4 + - - +
71D LEU* 2.6 44.6 + - + +
53G LYS* 4.4 15.3 - - - -
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Residues in contact with GLY 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 GLU 2.7 17.8 + - - -
65D LEU 2.9 4.7 + - - -
67D ASP* 1.3 74.3 - - - +
69D LEU* 1.3 61.5 + - - +
71D LEU* 3.4 6.8 + - - +
72D ASN* 3.3 26.1 + - - -
44G SER* 3.9 19.1 - - - -
52G TRP* 5.1 0.9 - - - -
53G LYS* 3.9 17.7 - - - +
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Residues in contact with LEU 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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8D LEU* 5.0 4.7 - - + -
36D ASP* 4.7 0.2 - - - +
38D VAL* 5.3 3.4 - - + -
65D LEU 2.9 19.5 + - - +
66D TYR* 3.6 21.3 - - + +
68D GLY* 1.3 70.8 - - - +
70D LYS* 1.3 70.9 + - - +
72D ASN 3.1 2.8 + - - -
73D HIS 3.0 14.7 + - - -
74D VAL* 3.2 28.5 + - + +
75D ASN* 4.4 10.5 - - + +
77D TYR* 3.5 22.9 - - + +
15G VAL* 4.3 16.6 - - + -
16G ARG* 4.0 19.3 - - + -
44G SER* 3.8 29.0 - - - +
45G ASN* 4.6 2.7 - - - +
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Residues in contact with LYS 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 TYR* 2.6 30.4 + - + +
67D ASP* 3.1 13.7 - - - +
69D LEU* 1.3 70.8 - - - +
71D LEU* 1.3 57.5 - - + +
73D HIS* 2.6 37.1 + - - -
75D ASN* 3.0 38.0 + - - +
100D GLU* 3.7 14.9 + - - +
104D GLN* 3.7 12.9 + - - +
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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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67D ASP* 2.6 28.7 + - + +
68D GLY* 3.5 7.2 - - - +
70D LYS* 1.3 73.8 - - + +
72D ASN* 1.3 59.5 + - - +
73D HIS* 3.7 16.5 + - - -
51G HIS* 3.9 47.0 + - + +
53G LYS* 3.3 41.3 - - + +
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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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68D GLY 3.3 18.0 + - - +
69D LEU 3.1 8.0 + - - +
70D LYS 2.9 0.2 + - - -
71D LEU* 1.3 75.4 - - - +
73D HIS* 1.3 80.0 + - - +
74D VAL* 3.5 17.2 + - + +
45G ASN* 3.5 13.3 + - - +
49G TYR* 3.8 16.6 - - + +
50G SER* 3.7 9.9 + - - -
51G HIS* 2.5 53.3 + - - +
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Residues in contact with HIS 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 LEU 3.0 0.2 + - - -
70D LYS* 2.6 27.8 + - - -
71D LEU* 3.9 15.0 + - - -
72D ASN* 1.3 82.3 - - - +
74D VAL* 1.3 61.2 + - - +
75D ASN* 3.4 9.6 - - - -
76D GLN* 3.5 18.1 - - - +
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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