Contacts of the helix formed by residues 41 - 56 (chain B) in PDB entry 2RD9
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 THR 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B HIS 3.7 7.0 - - - -
32B GLN* 3.2 36.4 + - - +
33B CYS 3.4 6.3 - - - -
34B ASN* 4.1 12.6 - - - +
39B THR 5.0 0.7 - - - +
40B TRP* 1.3 77.3 - - - +
42B VAL* 1.3 59.0 + - - +
43B TYR* 3.6 6.2 + - - +
44B GLU* 2.9 41.8 + - - +
45B VAL* 2.9 29.0 + - - +
86B ASN* 4.6 1.4 + - - +
153B SER* 5.6 0.2 - - - -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.6 35.2 - - + -
30B TRP 3.3 22.9 - - - +
31B HIS* 3.5 14.5 + - + +
33B CYS* 3.1 26.7 + - - +
41B THR* 1.3 72.8 - - - +
43B TYR* 1.3 64.6 + - - +
45B VAL* 3.2 11.8 + - - +
46B VAL* 3.2 14.3 + - + +
90B ILE* 5.1 0.7 - - + -
150B ILE* 3.7 39.0 - - + +
153B SER* 4.2 4.6 + - - -
154B MSE 4.1 3.1 - - + -
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 2.9 21.1 + - + +
32B GLN* 4.5 10.8 - - - +
41B THR* 3.2 4.9 - - - +
42B VAL* 1.3 75.6 - - - +
44B GLU* 1.3 59.2 + - - +
46B VAL* 3.2 6.2 + - - +
47B VAL* 3.0 47.6 + - + +
85B SER 3.3 13.2 + - - -
86B ASN* 3.4 47.1 + - - +
88B VAL 2.6 29.4 + - - -
90B ILE* 3.8 43.5 - - + -
93B ARG* 2.9 24.3 + - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR 4.5 0.7 - - - +
40B TRP* 3.4 24.6 - - + +
41B THR* 2.9 43.2 + - - +
43B TYR* 1.3 78.8 - - + +
45B VAL* 1.3 61.3 + - - +
47B VAL* 3.5 7.5 + - + +
48B HIS* 2.9 27.9 + - - +
86B ASN* 4.1 25.7 + - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 4.0 13.5 - - + +
41B THR 2.9 21.4 + - - +
42B VAL* 3.2 7.8 + - - +
44B GLU* 1.3 77.9 - - - +
46B VAL* 1.3 56.8 + - - +
48B HIS* 3.1 8.7 + - - +
49B LEU* 3.0 28.6 + - + +
146B HIS* 3.6 36.6 - - + +
149B GLN* 3.5 32.1 - - + +
150B ILE* 3.7 26.0 - - + +
153B SER* 6.1 0.4 - - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.4 12.1 - - + -
23B LEU* 4.3 15.5 - - + -
42B VAL* 3.4 14.4 - - + +
43B TYR* 3.2 9.5 + - - +
45B VAL* 1.3 72.3 - - - +
47B VAL* 1.3 66.7 + - - +
49B LEU* 3.2 9.9 + - - +
50B ILE* 3.0 26.3 + - + +
90B ILE* 4.8 4.9 - - + -
93B ARG* 4.2 25.6 - - + +
94B PHE* 4.3 20.6 - - + -
97B PHE* 5.2 7.6 - - + -
150B ILE* 4.0 17.7 - - + -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.0 43.6 + - + +
44B GLU* 3.7 10.1 - - + +
46B VAL* 1.3 74.8 - - - +
48B HIS* 1.3 59.1 + - - +
50B ILE* 3.1 13.1 + - + +
51B GLU* 2.9 29.0 + - + +
93B ARG* 3.9 31.6 - - + +
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Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ASP* 4.8 0.2 - - - -
40B TRP* 3.3 29.4 - + + -
44B GLU 2.9 15.5 + - - +
45B VAL 3.1 9.4 + - - +
47B VAL* 1.3 77.6 - - - +
49B LEU* 1.3 62.6 + - - +
51B GLU* 3.2 8.8 + - - +
52B ALA* 3.1 20.8 + - - +
142B HIS* 3.2 4.2 + + - -
146B HIS* 3.1 29.6 - + - -
300B NI 2.2 36.3 - - + +
-10C HIS* 3.5 24.2 + + - -
-9C HIS* 3.2 17.9 - + - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 4.9 5.4 - - + -
19B LEU* 3.7 29.6 - - + -
45B VAL* 3.0 20.6 + - + +
46B VAL* 3.6 10.3 - - - +
47B VAL 3.2 0.4 - - - -
48B HIS* 1.3 73.1 - - - +
50B ILE* 1.3 64.8 + - - +
52B ALA* 3.4 6.9 + - + +
53B GLU* 3.2 25.1 + - - +
97B PHE* 3.9 23.2 - - + -
142B HIS* 4.0 12.1 - - + +
143B ASP* 4.0 25.6 - - - +
146B HIS* 4.0 39.5 - - + -
147B ILE* 5.5 0.4 - - + +
150B ILE* 5.1 1.1 - - + -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.0 20.5 + - + +
47B VAL* 3.4 11.2 - - + +
49B LEU* 1.3 76.8 - - - +
51B GLU* 1.3 62.1 + - - +
53B GLU* 3.1 15.1 + - - +
54B LYS* 3.2 22.7 + - - +
93B ARG* 3.4 50.0 - - + +
96B GLU* 3.7 32.1 - - + +
97B PHE* 3.8 28.5 - - + +
100B LEU* 3.8 10.1 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 2.9 15.8 + - + +
48B HIS* 3.2 12.8 + - - +
50B ILE* 1.3 77.5 - - - +
52B ALA* 1.3 55.8 + - - +
54B LYS* 3.1 12.4 + - + +
55B THR* 2.9 40.9 + - + +
77B ASP* 5.2 6.1 - - - -
-11C HIS 5.8 0.7 - - - -
-10C HIS* 3.8 32.1 - - - +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS 3.1 9.6 + - - +
49B LEU* 3.7 8.7 - - + +
50B ILE 3.3 0.2 - - - -
51B GLU* 1.3 75.7 - - - +
53B GLU* 1.3 60.1 + - - +
56B ASN* 3.0 36.7 + - + +
57B TRP* 3.4 32.1 + - - +
142B HIS* 4.3 14.8 - - + +
-10C HIS* 3.6 21.4 - - + +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU 3.2 14.2 + - - +
50B ILE 3.1 9.9 + - - +
52B ALA* 1.3 77.5 - - - +
54B LYS* 1.3 61.3 + - - +
57B TRP* 3.8 6.4 + - - -
58B ILE* 5.2 0.9 + - - +
59B PRO* 5.0 5.9 - - - +
97B PHE* 3.7 20.0 - - + -
100B LEU* 3.8 21.4 - - + +
101B ARG* 2.9 48.0 + - - +
104B ASN* 2.6 50.3 + - - +
139B TRP* 3.3 15.5 + - - -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.2 18.0 + - + +
51B GLU* 3.1 14.4 + - + +
53B GLU* 1.3 78.3 - - - +
55B THR* 1.3 60.7 + - - +
59B PRO* 3.6 15.0 - - - +
93B ARG* 5.8 1.8 - - - +
96B GLU* 2.8 30.8 + - - -
100B LEU* 3.9 24.2 - - + -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 2.9 34.4 + - + +
54B LYS* 1.3 79.2 - - - +
56B ASN* 1.3 61.2 + - - +
59B PRO* 3.7 17.2 - - - +
60B ARG* 5.4 0.3 - - - +
76B PHE* 3.4 26.5 - - + +
77B ASP 4.8 3.8 + - - -
-10C HIS* 3.9 29.2 - - + +
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 3.0 26.7 + - + +
54B LYS 3.9 0.4 - - - -
55B THR* 1.3 77.2 - - - +
57B TRP* 1.3 91.3 + - + +
58B ILE 3.5 1.1 - - - -
59B PRO* 3.5 3.0 - - - +
60B ARG* 3.1 45.1 + - - +
76B PHE* 3.5 19.1 - - + -
-10C HIS* 2.9 26.1 + - - +
-9C HIS* 3.7 18.8 + - - -
-6C GLU* 5.1 1.2 + - - -
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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