Contacts of the helix formed by residues 40 - 57 (chain B) in PDB entry 3H2U
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 ASP 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B LEU* 1.3 80.4 - - - +
41B PRO* 1.3 79.9 - - - +
42B GLU* 3.3 21.1 + - - +
43B GLU* 4.0 15.4 - - + +
44B ILE* 2.9 24.8 + - - +
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Residues in contact with PRO 41 (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 LEU 5.3 0.2 - - - +
40B ASP* 1.3 96.6 - - - +
42B GLU* 1.3 71.7 + - + +
43B GLU 3.3 0.9 - - - -
44B ILE* 3.9 13.9 - - + +
45B ARG* 3.3 27.0 + - - +
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Residues in contact with GLU 42 (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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40B ASP* 3.3 13.7 + - - +
41B PRO* 1.3 92.9 - - + +
43B GLU* 1.3 61.1 + - - +
45B ARG* 2.5 41.0 + - - +
46B LYS* 3.3 24.5 + - - +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.5 12.6 - - + -
40B ASP* 3.9 21.1 + - + +
41B PRO 3.3 0.2 - - - -
42B GLU* 1.3 78.1 - - - +
44B ILE* 1.3 67.4 + - - +
46B LYS* 3.1 31.8 + - - +
47B ARG* 2.9 58.1 + - - +
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Residues in contact with ILE 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 LEU* 3.0 27.1 - - + +
40B ASP 2.9 23.7 + - - +
41B PRO* 4.0 9.9 - - + +
43B GLU* 1.3 79.1 - - - +
45B ARG* 1.3 66.3 + - + +
47B ARG* 3.4 5.7 + - - +
48B LEU* 3.1 29.6 + - + +
167B GLU 4.2 15.0 - - - +
168B ARG 3.0 23.3 - - - +
169B THR* 3.2 11.7 - - - +
170B GLY* 4.0 12.1 - - - -
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Residues in contact with ARG 45 (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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41B PRO 3.3 18.7 + - - +
42B GLU* 2.5 51.9 + - - +
43B GLU 3.2 0.8 - - - -
44B ILE* 1.3 82.6 - - + +
46B LYS* 1.3 64.3 + - - +
48B LEU* 3.8 5.3 - - - +
49B GLU* 2.8 68.2 + - - +
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Residues in contact with LYS 46 (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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42B GLU 3.3 17.7 + - - +
43B GLU* 3.1 38.5 + - - +
45B ARG* 1.3 84.7 - - - +
47B ARG* 1.3 65.8 + - + +
49B GLU* 3.3 10.5 - - - +
50B HIS* 2.9 31.3 + - + +
53B ARG* 5.2 1.6 + - - -
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Residues in contact with ARG 47 (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 LEU* 4.5 16.1 - - - +
43B GLU* 2.9 44.8 + - - +
44B ILE* 3.4 8.5 - - - +
46B LYS* 1.3 76.7 - - + +
48B LEU* 1.3 68.9 + - + +
49B GLU 3.0 0.9 - - - -
50B HIS* 2.8 19.0 + - - +
51B THR* 3.0 13.7 + - - -
144B THR* 5.9 5.3 - - - +
165B TYR* 3.7 45.1 + - + +
170B GLY 2.7 37.9 + - - +
171B GLN* 3.8 17.0 + - - +
172B SER* 4.1 3.0 - - - +
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Residues in contact with LEU 48 (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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44B ILE* 3.1 22.8 + - + +
45B ARG* 3.8 5.8 - - - +
47B ARG* 1.3 79.9 - - + +
49B GLU* 1.3 62.4 + - - +
51B THR* 3.6 9.1 + - + +
52B GLU* 3.3 25.6 + - - +
165B TYR* 3.8 36.6 - - + +
166B SER 4.1 4.0 - - - +
167B GLU* 3.4 50.9 - - - +
170B GLY* 5.3 0.7 - - - -
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Residues in contact with GLU 49 (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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45B ARG* 2.8 56.4 + - - +
46B LYS* 3.3 9.8 - - - +
47B ARG 3.0 0.2 - - - -
48B LEU* 1.3 73.8 - - - +
50B HIS* 1.3 64.6 - - - +
52B GLU* 3.1 8.6 + - - +
53B ARG* 3.1 42.5 + - + +
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Residues in contact with HIS 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 LYS* 2.9 14.9 + - + +
47B ARG* 2.8 15.1 + - - +
49B GLU* 1.3 68.2 - - - +
51B THR* 1.3 68.6 + - - +
52B GLU 3.2 0.2 + - - -
53B ARG* 3.3 32.1 + - + +
54B GLN* 3.0 49.5 + - + +
145B GLN* 4.3 34.2 + - + +
161B CYS 4.5 0.2 - - - -
165B TYR* 6.0 0.7 - - + -
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Residues in contact with THR 51 (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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47B ARG 3.0 8.3 + - - -
48B LEU* 3.8 12.6 - - + +
50B HIS* 1.3 78.0 + - - +
52B GLU* 1.3 61.6 + - + +
54B GLN* 3.3 2.4 + - - +
55B PHE* 2.8 28.7 + - + +
145B GLN* 4.8 1.6 + - - -
162B PHE* 3.9 26.7 - - + +
163B LEU 2.9 28.0 + - - +
164B VAL* 5.2 4.0 - - + -
165B TYR* 3.4 22.1 - - + +
218B LEU* 5.0 8.3 - - + -
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Residues in contact with GLU 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 LEU 3.3 12.0 + - - +
49B GLU* 3.1 12.6 + - - +
51B THR* 1.3 79.1 - - + +
53B ARG* 1.3 67.5 + - - +
54B GLN 3.0 1.6 - - - -
55B PHE* 3.1 18.5 + - - +
56B ARG* 2.8 65.9 + - + +
215B PRO* 4.0 16.2 - - - +
218B LEU* 5.7 1.6 - - - +
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Residues in contact with ARG 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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46B LYS 5.2 1.0 + - - -
49B GLU* 3.1 45.8 + - + +
50B HIS* 3.4 40.1 - - + +
52B GLU* 1.3 77.9 - - - +
54B GLN* 1.3 61.1 + - + +
56B ARG* 3.6 3.2 + - - +
57B ASN* 3.0 30.8 + - - +
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Residues in contact with GLN 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 HIS* 3.0 38.2 + - + +
51B THR 3.4 8.5 - - - +
53B ARG* 1.3 76.0 - - - +
55B PHE* 1.3 67.2 + - - +
56B ARG 3.0 2.6 + - - -
57B ASN* 3.2 10.1 + - - +
159B GLU 4.6 2.2 + - - -
160B ARG* 3.1 32.7 - - - +
161B CYS* 2.8 47.2 + - - +
162B PHE* 3.7 16.2 - - + -
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Residues in contact with PHE 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 THR* 2.8 19.7 + - + +
52B GLU* 3.1 22.6 + - - +
54B GLN* 1.3 73.8 - - - +
56B ARG* 1.3 78.0 + - + +
58B ARG* 3.9 4.7 - - - +
160B ARG* 3.0 33.1 + - - +
162B PHE* 3.8 32.0 - + + -
213B LEU* 3.5 31.9 - - + -
214B THR* 4.0 10.3 - - - -
215B PRO* 3.6 22.9 - - + -
218B LEU* 4.1 22.0 - - + -
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Residues in contact with ARG 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 GLU* 2.8 48.2 + - - +
53B ARG* 3.7 2.7 - - - +
55B PHE* 1.3 104.4 - - + +
57B ASN* 1.3 52.6 + - - +
58B ARG* 2.7 26.6 + - - +
103B GLY* 4.8 4.7 - - - -
215B PRO* 3.9 17.9 - - - +
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Residues in contact with ASN 57 (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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53B ARG 3.0 17.4 + - - +
54B GLN* 3.2 12.1 + - - +
56B ARG* 1.3 74.1 - - - +
58B ARG* 1.3 57.4 + - - +
59B ARG* 3.6 25.8 + - - +
101B LEU 5.1 0.4 + - - -
102B ASN* 3.7 10.5 - - - +
103B GLY* 3.3 23.2 + - - +
104B GLU* 4.5 4.3 - - - +
159B GLU* 4.4 13.5 + - - +
160B ARG* 3.7 18.9 - - + +
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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