Contacts of the helix formed by residues 41 - 56 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D HIS 3.7 11.0 - - - -
32D GLN* 3.3 34.4 + - - +
33D CYS 3.4 6.3 - - - -
34D ASN* 4.8 8.7 - - + +
39D THR 5.1 0.7 - - - +
40D TRP* 1.3 77.0 - - - +
42D VAL* 1.3 65.6 + - - +
43D TYR* 3.6 5.9 + - - +
44D GLU* 2.9 43.1 + - - +
45D VAL* 3.0 22.0 + - - +
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.0 25.8 - - + -
30D TRP 3.5 15.9 - - - +
31D HIS* 3.5 19.5 + - + +
33D CYS* 3.0 30.0 + - - +
41D THR* 1.3 72.5 - - - +
43D TYR* 1.3 62.8 + - - +
45D VAL* 3.1 6.4 + - - +
46D VAL* 3.1 22.4 + - + +
90D ILE* 5.0 0.4 - - + -
150D ILE* 3.9 47.4 - - + +
153D SER* 4.2 4.7 - - - -
154D MSE 4.0 3.4 - - + -
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Residues in contact with TYR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D HIS* 3.0 20.6 + - + +
32D GLN* 4.5 15.9 - - - +
41D THR* 3.2 5.1 - - - +
42D VAL* 1.3 72.2 - - - +
44D GLU* 1.3 65.7 + - + +
46D VAL* 3.2 5.2 + - - +
47D VAL* 3.0 42.0 + - + +
82D LEU* 4.1 15.5 - - + -
86D ASN* 3.4 10.0 - - - -
87D ALA* 5.6 3.4 - - + -
88D VAL 2.5 29.6 + - - -
90D ILE* 3.9 42.2 - - + -
93D ARG* 3.0 29.7 + - + -
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Residues in contact with GLU 44 (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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39D THR 4.5 1.2 - - - +
40D TRP* 3.3 22.6 - - + +
41D THR* 2.9 42.4 + - - +
43D TYR* 1.3 82.9 - - + +
45D VAL* 1.3 61.1 + - - +
47D VAL* 4.4 1.1 - - - -
48D HIS* 2.9 24.3 + - - +
82D LEU* 4.8 8.0 - - + +
302D GOL 3.1 34.8 - - - +
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D TRP* 4.0 15.7 - - + +
41D THR 3.0 17.6 + - - +
42D VAL* 3.1 9.8 + - - +
44D GLU* 1.3 76.3 - - - +
46D VAL* 1.3 58.9 + - - +
48D HIS* 3.2 7.8 + - - +
49D LEU* 3.0 30.2 + - + +
146D HIS* 3.6 37.9 - - + +
149D GLN* 3.7 28.0 - - + +
150D ILE* 3.7 24.0 - - + -
153D SER* 6.0 0.4 - - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.6 6.5 - - + -
23D LEU* 4.2 24.2 - - + -
42D VAL 3.1 16.2 + - - +
43D TYR* 3.2 7.8 + - - +
45D VAL* 1.3 74.3 - - - +
47D VAL* 1.3 63.2 + - - +
49D LEU* 3.2 12.3 + - - +
50D ILE* 3.2 25.3 + - + +
90D ILE* 4.5 7.9 - - + -
93D ARG* 3.8 28.7 - - + +
94D PHE* 4.2 22.2 - - + -
97D PHE* 5.3 8.5 - - + -
150D ILE* 4.3 8.1 - - + -
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Residues in contact with VAL 47 (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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43D TYR* 3.0 44.1 + - + +
44D GLU 3.9 0.2 - - - +
45D VAL 3.5 0.2 - - - -
46D VAL* 1.3 71.4 - - - +
48D HIS* 1.3 57.8 + - - +
50D ILE* 3.1 15.0 + - + +
51D GLU* 3.0 45.6 + - + +
82D LEU* 4.0 21.5 - - + -
93D ARG* 3.8 28.3 - - + +
302D GOL 3.8 16.4 - - - +
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Residues in contact with HIS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-10A HIS* 3.3 32.0 + + - -
-9A HIS* 3.4 10.5 - + - -
174C ASP* 4.7 0.2 - - - -
40D TRP* 3.3 27.1 - + + -
44D GLU 2.9 19.0 + - - +
45D VAL 3.4 4.5 - - - +
47D VAL* 1.3 77.7 - - - +
49D LEU* 1.3 59.9 + - - +
51D GLU* 3.2 10.9 + - - +
52D ALA* 2.9 27.9 + - - +
142D HIS* 3.1 6.5 + + - -
146D HIS* 3.2 29.8 - + - -
300D NI 2.2 36.2 - - + +
302D GOL 3.9 8.8 + - - -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D THR* 4.7 5.4 - - + -
19D LEU* 3.6 31.2 - - + -
45D VAL* 3.0 19.9 + - + +
46D VAL* 3.2 10.7 + - - +
48D HIS* 1.3 75.7 - - - +
50D ILE* 1.3 63.8 + - - +
52D ALA* 3.5 6.3 + - + +
53D GLU* 3.1 26.9 + - - +
97D PHE* 4.0 24.6 - - + -
101D ARG* 5.5 0.7 - - - +
142D HIS* 4.0 27.1 - - + +
143D ASP* 4.2 19.7 - - - +
146D HIS* 4.0 26.7 - - + -
147D ILE* 5.7 0.7 - - + +
150D ILE* 5.2 0.9 - - + -
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Residues in contact with ILE 50 (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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46D VAL* 3.2 16.7 + - + +
47D VAL* 3.1 14.9 + - + +
49D LEU* 1.3 76.8 - - - +
51D GLU* 1.3 58.8 + - + +
53D GLU* 3.0 22.7 + - - +
54D LYS* 3.2 22.5 + - + +
93D ARG* 3.4 47.3 - - + +
96D GLU* 3.7 37.0 - - + +
97D PHE* 3.8 27.8 - - + +
100D LEU* 3.8 8.2 - - + +
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Residues in contact with GLU 51 (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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-12A HIS* 3.2 22.8 + - - -
-10A HIS* 4.1 12.3 + - - +
47D VAL* 3.0 32.7 + - + +
48D HIS* 3.5 9.6 - - - +
50D ILE* 1.3 77.3 - - + +
52D ALA* 1.3 58.6 + - - +
54D LYS* 3.1 5.2 + - + +
55D THR* 2.9 33.1 + - - +
79D PHE* 3.5 48.8 - - + +
80D SER 5.1 0.5 - - - +
82D LEU* 5.3 1.7 - - - +
302D GOL 2.9 25.2 + - - -
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Residues in contact with ALA 52 (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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-10A HIS* 3.5 25.4 - - + +
48D HIS 2.9 15.9 + - - +
49D LEU* 3.6 6.7 - - + +
51D GLU* 1.3 76.5 - - - +
53D GLU* 1.3 63.7 + - - +
56D ASN* 3.0 25.6 + - + +
57D TRP* 3.6 31.0 + - - +
142D HIS* 4.0 14.6 - - + +
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Residues in contact with GLU 53 (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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49D LEU 3.1 15.5 + - - +
50D ILE 3.0 10.3 + - - +
52D ALA* 1.3 77.2 - - - +
54D LYS* 1.3 59.7 + - - +
57D TRP* 3.8 6.6 + - - -
58D ILE* 5.3 1.0 + - - +
59D PRO* 4.9 6.2 - - - +
97D PHE* 3.7 19.3 - - + -
100D LEU* 3.8 19.7 - - + +
101D ARG* 2.9 48.6 + - - +
104D ASN* 2.7 47.4 + - - +
139D TRP* 3.3 16.3 + - - -
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Residues in contact with LYS 54 (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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50D ILE* 3.2 18.8 + - + +
51D GLU* 3.1 8.9 + - + +
53D GLU* 1.3 79.5 - - - +
55D THR* 1.3 60.0 + - - +
56D ASN 3.8 0.2 - - - -
59D PRO* 3.7 13.1 - - - +
77D ASP* 4.9 3.4 - - - +
79D PHE* 4.2 23.7 - - + -
93D ARG* 6.1 0.2 - - - +
96D GLU* 2.7 31.1 + - - -
100D LEU* 3.9 24.2 - - + -
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Residues in contact with THR 55 (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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-10A HIS* 3.8 24.7 - - + -
51D GLU 2.9 18.5 + - - +
54D LYS* 1.3 76.3 - - - +
56D ASN* 1.3 62.2 + - - +
59D PRO* 3.6 19.4 - - - +
60D ARG* 5.3 0.9 - - - +
76D PHE* 3.6 19.0 - - + -
77D ASP* 2.9 45.0 + - - +
79D PHE* 3.9 17.5 - - + -
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Residues in contact with ASN 56 (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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-10A HIS* 3.0 32.7 + - - +
-9A HIS* 3.5 21.4 + - - -
-6A GLU* 5.1 0.4 + - - -
52D ALA* 3.0 17.0 + - + +
54D LYS 3.8 0.6 - - - -
55D THR* 1.3 78.6 - - - +
57D TRP* 1.3 95.2 + - + +
58D ILE 3.6 1.3 - - - -
59D PRO* 3.7 2.3 - - - +
60D ARG* 3.0 35.7 + - - +
76D PHE* 3.6 23.5 - - + -
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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
------------------------------------------------------------
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