Contacts of the helix formed by residues 62 - 74 (chain U) in PDB entry 3RWR
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 62 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60U ALA 4.4 0.4 + - - -
61U MET* 1.3 76.1 - - - +
63U LYS* 1.3 66.7 + - - +
64U GLY* 3.0 5.7 + - - +
65U LYS* 4.5 11.7 - - + +
66U TYR* 3.0 18.2 + - - +
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Residues in contact with LYS 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U GLU* 4.9 13.0 - - + +
49U GLU* 4.2 25.8 + - + +
52U ILE* 4.7 10.3 - - + -
53U SER* 3.7 31.3 + - - +
56U ALA* 4.3 12.2 - - + +
61U MET 3.5 1.0 + - - -
62U GLU* 1.3 71.2 - - - +
64U GLY* 1.3 61.0 + - - +
66U TYR* 4.1 0.3 - - - +
67U VAL* 2.9 42.6 + - + +
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Residues in contact with GLY 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U GLU* 4.9 13.0 + - - -
62U GLU* 3.1 3.4 - - - +
63U LYS* 1.3 79.1 - - - +
65U LYS* 1.3 66.5 + - - +
67U VAL* 3.2 4.7 + - - +
68U GLY* 3.0 19.9 + - - -
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Residues in contact with LYS 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61U MET* 4.3 19.9 - - + +
62U GLU* 3.3 20.6 + - + +
64U GLY* 1.3 72.4 - - - +
66U TYR* 1.3 66.7 + - - +
68U GLY* 3.1 12.8 + - - -
69U GLU* 3.6 26.9 + - - +
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Residues in contact with TYR 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U ILE* 3.8 27.9 - - + +
55U GLU* 3.1 19.8 - - + +
56U ALA* 3.7 19.3 - - + -
59U MET* 4.1 23.3 - - + -
61U MET* 3.7 28.8 - - + +
62U GLU 3.0 16.8 + - - +
63U LYS 4.1 0.9 - - - +
65U LYS* 1.3 76.7 - - - +
67U VAL* 1.3 82.8 + - + +
68U GLY 2.9 1.6 + - - -
69U GLU* 2.9 24.4 + - + +
70U LEU* 3.7 24.7 + - + +
108U LEU* 3.6 11.7 + - + -
109U GLY* 3.0 40.0 + - - -
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Residues in contact with VAL 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U LEU* 4.2 17.0 - - + -
29U GLU* 3.6 33.2 - - + +
52U ILE* 3.4 33.7 - - + -
63U LYS* 2.9 25.8 + - + +
64U GLY 3.7 3.1 - - - +
66U TYR* 1.3 80.5 - - + +
68U GLY* 1.3 64.2 + - - +
70U LEU* 2.9 38.3 + - + +
71U ARG* 3.4 14.4 + - - +
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Residues in contact with GLY 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64U GLY 3.0 12.0 + - - -
65U LYS* 3.5 7.6 - - - -
66U TYR 2.9 3.4 + - - -
67U VAL* 1.3 77.5 - - - +
69U GLU* 1.3 62.0 + - - +
71U ARG* 2.9 31.8 + - - +
72U LYS* 3.4 13.6 + - - +
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Residues in contact with GLU 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59U MET* 6.1 2.0 - - + -
61U MET* 4.5 15.5 - - + -
65U LYS* 3.6 25.9 + - - +
66U TYR* 2.9 18.6 + - + +
68U GLY* 1.3 70.7 - - - -
70U LEU* 1.3 57.7 + - + +
72U LYS* 3.0 23.3 + - - +
73U ALA* 2.8 30.5 + - - +
84U TYR* 2.6 31.7 + - - +
99U LYS* 2.6 30.0 + - + +
108U LEU* 4.3 14.4 - - + -
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Residues in contact with LEU 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U LEU* 4.0 13.0 - - + -
32U PHE* 4.5 11.0 - - + -
52U ILE* 3.8 28.5 - - + -
66U TYR* 3.8 28.3 - - + +
67U VAL* 2.9 41.9 + - + +
69U GLU* 1.3 77.4 - - + +
71U ARG* 1.3 53.0 + - - +
73U ALA* 2.8 4.6 + - - -
74U LEU* 2.6 48.6 + - + +
75U LEU* 4.3 0.2 - - - +
97U PHE* 4.1 23.3 - - + -
108U LEU* 4.3 4.3 - - + +
109U GLY 5.0 1.3 - - - +
111U PHE* 6.3 1.1 - - + -
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Residues in contact with ARG 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U THR* 3.6 34.9 - - - +
28U LEU* 3.7 19.2 - - + +
29U GLU* 3.6 29.3 + - - +
67U VAL* 3.6 15.8 - - - +
68U GLY* 2.9 17.6 + - - +
70U LEU* 1.3 74.4 - - - +
72U LYS* 1.3 61.1 + - + +
73U ALA 3.4 0.2 - - - -
75U LEU* 2.9 47.3 - - + +
77U GLY* 4.0 3.1 + - - -
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Residues in contact with LYS 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U GLY 4.0 14.4 - - - +
69U GLU* 3.0 39.2 + - - +
70U LEU 3.0 0.8 - - - -
71U ARG* 1.3 79.6 - - + +
73U ALA* 1.3 60.1 + - - +
76U SER* 4.7 0.2 - - - -
77U GLY* 3.1 38.9 + - - +
78U ALA* 3.9 3.2 + - + +
82U ASP* 5.3 2.6 + - - -
84U TYR* 3.1 19.0 + - + +
99U LYS* 3.6 11.3 - - - +
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Residues in contact with ALA 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U GLU 2.8 14.2 + - - +
70U LEU* 2.8 4.8 + - - +
72U LYS* 1.3 80.7 - - - +
74U LEU* 1.3 59.1 + - + +
75U LEU 3.5 0.6 + - - -
76U SER* 4.5 4.2 + - - -
84U TYR* 3.4 34.5 - - + +
86U PHE* 3.0 26.6 - - - -
97U PHE* 3.6 25.6 - - + -
108U LEU* 4.7 0.4 - - + -
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Residues in contact with LEU 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U LYS 5.1 0.7 - - - +
6U SER* 5.3 6.0 - - - -
20U LEU* 4.7 15.8 - - + +
22U VAL* 3.1 35.6 - - + +
28U LEU* 6.0 1.3 - - + -
32U PHE* 4.5 14.4 - - + -
34U ILE* 5.0 4.9 - - + -
70U LEU* 2.6 38.7 + - + +
73U ALA* 1.3 74.5 - - - +
75U LEU* 1.3 59.8 + - + +
76U SER 3.6 1.8 - - - -
86U PHE* 5.0 3.1 - - + -
95U PHE* 4.6 14.8 - - + -
97U PHE* 3.5 42.6 - - + -
111U PHE* 4.4 19.7 - - + -
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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