Contacts of the helix formed by residues 68 - 80 (chain H) 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 PRO 68 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B ASP 4.4 6.1 - - - +
604B VAL* 3.3 28.5 - - + -
66H THR 4.4 1.1 - - - +
67H ALA* 1.3 85.3 - - - +
69H PRO* 1.3 74.4 - - + +
70H ALA* 3.1 3.6 + - + +
71H ALA* 4.0 15.3 - - + +
72H PHE* 3.3 20.8 + - - +
14R PRO* 5.4 10.8 - - + -
15R SER* 5.8 3.6 - - - +
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Residues in contact with PRO 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H THR* 4.3 11.3 - - - +
54H VAL* 3.7 27.2 - - - +
55H SER* 2.9 37.9 - - - +
67H ALA 3.9 1.1 - - - +
68H PRO* 1.3 84.6 - - + +
70H ALA* 1.3 59.2 - - - +
72H PHE* 4.1 2.7 - - + +
73H LEU* 4.3 2.3 - - - +
11R VAL* 4.6 19.5 - - + +
14R PRO* 5.3 10.8 - - + -
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Residues in contact with ALA 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LYS* 3.6 25.2 - - + +
51H THR* 4.8 4.7 - - + -
68H PRO* 3.2 1.9 - - + +
69H PRO* 1.3 76.2 - - - +
71H ALA* 1.3 67.0 + - - +
72H PHE 3.2 2.8 + - - -
73H LEU* 3.4 17.4 + - - +
74H CYS* 3.1 16.3 + - - -
11R VAL 3.6 21.3 + - - +
12R SER* 4.0 13.5 - - - +
14R PRO* 5.7 1.8 - - + +
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Residues in contact with ALA 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B ASP* 4.3 25.5 - - + +
604B VAL* 4.5 2.9 - - + -
68H PRO* 3.3 29.5 + - + +
70H ALA* 1.3 75.2 - - - +
72H PHE* 1.3 68.5 + - - +
74H CYS* 2.9 29.9 + - - +
75H HIS* 3.1 7.3 + - - +
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Residues in contact with PHE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B VAL* 6.1 0.2 - - - -
54H VAL* 4.2 13.9 - - + -
55H SER* 5.7 0.4 - - - +
58H ALA* 3.5 36.6 - - + -
62H ASN* 4.0 17.7 - - - -
65H LEU* 4.8 6.7 - - + -
67H ALA* 4.8 19.9 - - + +
68H PRO 3.3 13.0 + - - +
69H PRO* 4.1 9.2 - - + +
70H ALA 3.2 0.2 - - - -
71H ALA* 1.3 76.3 - - - +
73H LEU* 1.3 66.8 + - - +
75H HIS* 2.9 7.9 + - - +
76H LEU* 2.9 41.0 + - + -
117H PHE* 3.4 38.8 - + - -
118H TYR 4.1 3.8 - - - -
119H TRP* 4.2 17.7 - + - -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ILE* 3.6 9.4 - - + +
30H THR 3.7 16.2 - - - +
31H LYS 4.4 4.3 - - - +
32H GLN 4.1 1.6 - - - -
33H GLY* 3.2 35.4 - - - +
34H TYR* 3.4 36.1 - - + -
51H THR* 4.8 2.0 - - - -
54H VAL* 3.4 37.9 - - + -
69H PRO 4.3 4.3 - - - +
70H ALA 3.4 10.7 + - - +
71H ALA 3.4 0.6 - - - -
72H PHE* 1.3 81.6 - - - +
74H CYS* 1.3 54.6 - - - +
76H LEU* 3.9 8.5 - - + +
77H ASP* 2.8 36.2 + - - +
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Residues in contact with CYS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B ASP* 4.6 8.5 - - - +
29H ILE* 5.5 0.2 - - - -
30H THR 5.3 1.3 - - - -
31H LYS* 4.7 24.9 - - + -
70H ALA* 3.1 22.9 - - - -
71H ALA* 2.9 19.9 + - - +
73H LEU* 1.3 77.7 - - - +
75H HIS* 1.3 54.0 + - - +
77H ASP* 3.4 7.4 - - - +
78H ASN* 2.6 29.8 - - - +
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Residues in contact with HIS 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B LEU* 4.5 14.4 - - + +
602B LYS* 4.8 12.9 + - + +
603B ASP* 4.5 18.6 + - + +
604B VAL* 6.3 1.3 - - + -
71H ALA 3.1 7.2 + - - +
72H PHE* 2.9 9.6 + - - +
74H CYS* 1.3 73.2 - - - +
76H LEU* 1.3 67.1 + - - +
77H ASP 3.0 1.3 - - - -
78H ASN* 2.9 21.3 + - + +
79H LEU* 3.1 10.6 + - - +
112H LEU* 3.3 43.9 - - + +
113H SER 6.1 0.4 - - - -
117H PHE* 5.0 2.9 - - + -
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ILE* 4.3 12.3 - - + -
34H TYR* 4.5 10.1 - - + -
72H PHE* 2.9 32.5 + - + +
73H LEU* 3.9 8.1 - - + +
75H HIS* 1.3 76.3 - - - +
77H ASP* 1.3 63.3 + - - +
79H LEU* 3.0 35.3 + - + +
80H LEU* 3.2 22.9 + - + +
108H VAL* 5.3 1.8 - - + -
117H PHE* 4.2 9.7 - - + -
119H TRP* 3.0 52.5 - - + +
121H PHE* 5.0 1.6 - - + -
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ILE* 3.0 48.9 + - + +
73H LEU 2.8 21.7 + - - +
74H CYS* 3.4 10.1 - - - +
75H HIS 3.0 0.2 - - - -
76H LEU* 1.3 78.9 - - - +
78H ASN* 1.3 68.0 + - - +
79H LEU 3.4 0.2 + - - -
80H LEU* 3.5 18.6 + - - +
81H ARG* 4.6 3.8 + - - -
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Residues in contact with ASN 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H CYS 2.6 25.8 - - - +
75H HIS* 2.9 15.1 + - + +
77H ASP* 1.3 81.9 - - - +
79H LEU* 1.3 64.6 + - - +
81H ARG* 3.4 20.2 - - - +
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H HIS* 3.1 8.0 + - - +
76H LEU* 3.0 21.4 + - + +
78H ASN* 1.3 79.4 - - - +
80H LEU* 1.3 81.1 + - + +
81H ARG* 2.9 10.9 + - - +
82H PRO* 4.1 4.9 - - + +
90H PRO* 5.4 4.2 - - - +
93H ALA* 5.5 3.8 - - + -
95H PHE* 5.1 2.9 - - + -
108H VAL* 4.3 16.6 - - + -
110H SER* 3.0 33.0 - - - +
111H GLU 4.7 2.7 - - - +
112H LEU* 5.1 4.3 - - + -
117H PHE* 3.4 29.6 - - + +
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H VAL* 4.2 26.5 - - + -
29H ILE* 4.3 12.8 - - + -
36H LEU* 6.4 0.4 - - + -
76H LEU* 3.2 20.3 + - + +
77H ASP 3.5 10.6 + - - +
78H ASN 3.3 0.6 - - - -
79H LEU* 1.3 88.5 - - + +
81H ARG* 1.3 85.8 + - - +
82H PRO* 3.4 6.5 - - + -
83H LEU* 4.1 9.9 - - + -
95H PHE* 3.4 37.9 - - + -
108H VAL* 5.1 3.8 - - + -
121H PHE* 4.2 18.6 - - + -
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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