Contacts of the helix formed by residues 42 - 54 (chain B) in PDB entry 1SVU
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B GLU* 3.6 10.9 - - - +
41B TRP* 1.3 81.0 - - + +
43B LYS* 1.3 68.8 + - - +
44B TYR* 2.9 47.1 + - - +
45B ALA* 3.1 14.6 + - + -
46B GLN* 3.1 15.7 + - - +
297B GLN* 5.0 0.9 - - - +
301B GLN* 4.1 3.1 + - - -
402B SAH 4.0 14.8 - - - +
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Residues in contact with LYS 43 (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 TRP 3.2 5.0 + - - -
42B ASP* 1.3 73.3 + - - +
44B TYR* 1.3 74.3 + - + +
46B GLN* 3.8 13.1 - - - +
47B GLU* 3.0 25.1 + - - +
56B LYS* 5.6 0.3 - - - +
404B UNX 3.7 4.1 - - - -
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Residues in contact with TYR 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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42B ASP* 2.9 24.1 + - - +
43B LYS* 1.3 88.1 - - + +
45B ALA* 1.3 69.0 + - - +
47B GLU* 2.7 17.9 - - - +
48B VAL* 2.8 10.2 + - - +
292B HIS* 3.1 25.4 - + + +
294B SER* 6.0 1.6 - - - -
297B GLN* 3.2 34.8 - - + -
301B GLN* 3.0 18.4 - - - +
404B UNX 4.6 4.3 - - - -
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Residues in contact with ALA 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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20B GLY* 3.7 18.4 - - - +
21B LEU* 5.5 1.1 - - + -
40B GLU* 3.4 37.5 - - + +
42B ASP* 3.1 11.1 + - + +
44B TYR* 1.3 76.2 - - - +
46B GLN* 1.3 55.6 + - - +
48B VAL* 2.5 29.5 + - - -
49B TYR* 2.7 15.9 + - - +
301B GLN* 3.3 12.4 - - - +
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Residues in contact with GLN 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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40B GLU* 2.6 30.4 + - - +
41B TRP* 2.9 26.4 + - - +
42B ASP 3.1 11.9 + - - +
43B LYS* 3.8 11.1 - - - +
45B ALA* 1.3 76.6 - - - +
47B GLU* 1.3 65.9 + - - +
49B TYR* 4.3 0.4 - - - +
50B GLU* 3.0 24.3 + - - +
56B LYS* 3.1 43.5 + - + +
57B PRO* 3.9 26.2 + - + +
59B GLY* 4.6 6.1 - - - -
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Residues in contact with GLU 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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43B LYS 3.0 12.0 + - - +
44B TYR* 2.7 19.7 + - - +
45B ALA 2.6 4.2 + - - -
46B GLN* 1.3 76.9 - - - +
48B VAL* 1.3 56.4 + - + +
50B GLU* 3.2 13.0 - - - +
51B MET* 2.9 24.0 - - + +
56B LYS* 5.2 0.9 - - - -
292B HIS* 4.1 9.4 - - + +
293B PRO* 6.0 1.1 - - + -
404B UNX 2.8 29.6 - - - -
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Residues in contact with VAL 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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21B LEU* 4.0 7.0 - - + -
44B TYR 2.8 9.3 + - - +
45B ALA 2.5 11.2 + - - +
47B GLU* 1.3 66.8 - - - +
49B TYR* 1.3 62.7 + - - +
50B GLU 2.8 6.9 + - - -
51B MET* 3.0 12.4 + - + -
52B ASN* 2.8 50.7 + - - +
289B TYR* 3.0 24.5 - - + +
290B LYS 3.2 10.5 - - - +
292B HIS* 3.6 29.4 - - + +
301B GLN* 3.3 23.3 - - - +
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Residues in contact with TYR 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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16B ASP* 3.3 20.7 + - - +
19B ALA* 3.2 31.0 - - + -
20B GLY 3.7 5.9 + - - +
22B GLY* 3.2 28.5 - - - -
25B ARG* 2.9 29.3 + - - -
35B CYS* 3.8 0.7 - - - -
38B SER* 3.6 23.8 - - - -
45B ALA 2.7 18.5 + - - +
48B VAL* 1.3 73.6 - - - +
50B GLU* 1.3 56.3 + - - +
52B ASN* 4.8 0.4 - - - -
53B PHE* 2.8 51.4 + + + +
55B GLU* 3.1 12.8 - - + +
57B PRO* 3.2 30.3 - - + -
289B TYR* 4.6 2.2 + - - -
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Residues in contact with GLU 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 GLN 3.0 16.6 + - - +
47B GLU* 3.2 8.2 - - - +
48B VAL 2.8 1.0 + - - -
49B TYR* 1.3 73.2 - - - +
51B MET* 1.3 58.8 + - + +
52B ASN 2.7 13.3 + - - -
54B GLY* 2.9 29.0 + - - +
55B GLU* 2.7 21.2 + - - +
56B LYS* 2.7 43.2 + - - +
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Residues in contact with MET 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 GLU* 2.9 22.0 - - - +
48B VAL* 3.3 19.5 - - + +
50B GLU* 1.3 74.8 - - + +
52B ASN* 1.3 59.8 + - - +
54B GLY 4.8 1.2 + - - -
290B LYS* 3.7 30.9 - - + +
291B VAL 3.4 25.8 - - - +
293B PRO* 3.7 23.6 - - + -
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Residues in contact with ASN 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 VAL* 2.8 49.9 + - - +
49B TYR 4.4 0.4 - - - +
50B GLU 2.7 4.4 + - - -
51B MET* 1.3 75.4 - - - +
53B PHE* 1.3 72.7 + - + +
54B GLY 3.6 1.1 + - - -
288B SER 4.0 1.6 - - - +
289B TYR* 3.1 32.2 - - + -
290B LYS* 2.5 44.6 + - - +
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Residues in contact with PHE 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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21B LEU 3.4 11.7 - - - -
22B GLY* 3.4 42.4 - - - -
25B ARG* 3.3 44.8 + - + +
26B LEU* 4.6 16.2 - - + -
29B GLU* 4.9 4.5 - - - -
49B TYR* 2.8 52.9 + + + +
52B ASN* 1.3 82.9 - - + +
54B GLY* 1.3 57.2 + - - +
55B GLU* 2.8 21.1 + - - +
289B TYR* 4.0 15.3 - + - -
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Residues in contact with GLY 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 GLU* 2.9 16.4 + - - +
51B MET 4.7 1.2 + - - -
52B ASN 3.6 2.4 + - - -
53B PHE* 1.3 74.2 - - - +
55B GLU* 1.3 56.9 + - - +
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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