Contacts of the helix formed by residues 41 - 56 (chain B) in PDB entry 4NKT
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 HIS 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ASP 5.3 0.8 + - - -
39B MET 3.2 0.4 - - - -
40B SER* 1.3 100.7 + - - +
42B LYS* 1.3 57.2 + - - +
43B GLU 3.5 2.0 - - - -
44B PHE* 4.1 16.8 - + + -
45B THR* 2.8 29.7 + - - -
267B SER* 3.8 5.5 + - - +
269B GLY* 3.9 13.2 - - - -
270B SER* 2.8 46.3 + - - +
273B HIS* 2.7 37.6 + + + -
361B LEU* 5.8 2.5 - - + -
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Residues in contact with LYS 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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38B ASP 5.9 0.2 + - - -
39B MET* 3.9 28.4 + - + +
40B SER 3.8 2.0 + - - -
41B HIS* 1.3 76.9 - - - +
43B GLU* 1.3 61.1 + - + +
45B THR* 3.5 5.7 + - - -
46B LYS* 3.1 27.1 + - + +
267B SER* 6.2 0.4 - - - -
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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
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41B HIS 3.5 0.2 - - - -
42B LYS* 1.3 78.3 - - + +
44B PHE* 1.3 65.3 - - - +
46B LYS* 3.3 10.6 + - + +
47B PHE* 3.1 23.0 + - - +
367B PRO* 4.5 18.0 - - - +
368B ILE 5.5 0.5 + - - -
370B TYR* 4.1 22.1 + - + +
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Residues in contact with PHE 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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41B HIS* 3.6 21.4 + + + +
43B GLU* 1.3 78.0 - - - +
45B THR* 1.3 57.9 + - - +
47B PHE* 3.2 12.1 + + - +
48B CYS* 2.9 48.1 + - - -
269B GLY* 3.5 33.7 - - - -
272B LEU* 4.1 13.9 - - + -
276B PHE* 5.1 0.2 - + - -
361B LEU* 3.8 31.0 - - + -
370B TYR* 3.4 48.1 + + + +
373B LEU* 3.9 25.1 - - + -
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Residues in contact with THR 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 HIS 2.8 22.3 + - - -
42B LYS* 3.7 5.6 - - - -
44B PHE* 1.3 77.2 - - - +
46B LYS* 1.3 62.3 + - - +
48B CYS* 3.0 14.0 + - - +
49B TYR* 3.1 40.2 + - + -
267B SER* 3.0 17.1 + - - -
268B LEU* 4.2 2.7 - - + +
269B GLY* 2.9 29.5 + - - +
405B MG 3.7 17.0 - - - -
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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 LYS* 3.1 17.9 + - + +
43B GLU* 3.6 10.3 - - + +
44B PHE 3.3 0.2 - - - -
45B THR* 1.3 77.3 - - - +
47B PHE* 1.3 61.1 + - - +
49B TYR* 3.5 5.7 + - - +
50B GLU* 3.3 42.2 + - + +
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Residues in contact with PHE 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 GLU 3.1 13.2 + - - +
44B PHE* 3.4 20.4 - + - +
46B LYS* 1.3 74.5 - - - +
48B CYS* 1.3 68.9 + - - +
50B GLU* 3.2 18.8 + - + +
51B VAL* 3.0 43.2 + - + +
370B TYR* 3.5 50.3 - + + -
371B ASP* 3.8 25.6 - - - -
373B LEU* 5.3 0.4 - - + -
374B PHE* 3.6 27.8 - + - -
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Residues in contact with CYS 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 PHE* 2.9 55.3 + - - -
45B THR* 3.0 11.4 + - - +
47B PHE* 1.3 79.4 - - - +
49B TYR* 1.3 58.3 + - - +
51B VAL* 3.4 3.5 + - - +
52B TYR* 2.8 28.6 + - - +
191B LEU* 3.6 21.6 - - + +
268B LEU* 3.7 13.2 - - + -
269B GLY* 4.6 3.6 - - - -
272B LEU* 3.6 20.6 - - - -
374B PHE* 5.9 2.9 - - - -
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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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45B THR* 3.1 48.3 + - + +
46B LYS* 4.1 5.8 - - - +
47B PHE 3.3 0.2 - - - -
48B CYS* 1.3 74.5 - - - +
50B GLU* 1.3 57.1 + - - +
52B TYR* 3.6 19.7 - + - +
53B ASN* 2.7 45.3 + - - +
183B ALA 5.2 1.5 + - - -
184B ARG* 4.4 13.7 - - - +
187B PRO* 4.0 15.6 - - + +
268B LEU* 3.5 33.9 + - + +
405B MG 4.2 8.1 - - - -
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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 LYS* 3.3 42.5 + - + +
47B PHE* 3.2 22.7 + - + +
49B TYR* 1.3 78.1 - - - +
51B VAL* 1.3 62.5 + - + +
53B ASN* 3.3 15.0 + - - +
54B GLU* 3.3 23.4 + - - +
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Residues in contact with VAL 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 PHE* 3.0 55.4 + - + +
48B CYS 3.8 4.0 - - - +
50B GLU* 1.3 73.9 - - + +
52B TYR* 1.3 67.3 + - - +
54B GLU* 3.0 18.8 + - + +
55B ILE* 3.1 18.0 + - + +
191B LEU* 3.6 20.2 - - + -
194B HIS* 4.0 19.3 - - + +
374B PHE* 3.9 13.0 - - + -
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Residues in contact with TYR 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 CYS 2.8 18.5 + - - +
49B TYR* 3.6 23.8 - + - +
51B VAL* 1.3 76.5 - - - +
53B ASN* 1.3 72.2 + - - +
54B GLU 3.2 0.2 + - - -
55B ILE* 3.2 7.7 + - - +
56B LYS* 3.1 55.8 + - + +
186B LYS* 3.3 31.5 + - + +
187B PRO* 3.6 37.9 - - + -
190B LEU* 3.7 27.6 - - + -
191B LEU* 4.0 8.0 - - + +
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Residues in contact with ASN 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 TYR* 2.7 34.9 + - - +
50B GLU* 3.7 8.1 - - - +
51B VAL 3.2 0.2 - - - -
52B TYR* 1.3 85.1 - - - +
54B GLU* 1.3 61.5 + - + +
56B LYS* 2.7 46.3 + - - +
98B LYS* 5.1 1.6 + - - -
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Residues in contact with GLU 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* 3.3 19.0 + - - +
51B VAL* 3.0 12.6 + - + +
53B ASN* 1.3 79.7 - - + +
55B ILE* 1.3 62.7 + - + +
56B LYS 3.6 0.2 - - - -
98B LYS* 3.0 28.3 + - - +
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Residues in contact with ILE 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 VAL* 3.1 17.0 + - + +
52B TYR* 3.6 7.2 - - - +
54B GLU* 1.3 82.9 - - + +
56B LYS* 1.3 71.8 + - - +
97B LEU* 3.5 19.0 - - + +
98B LYS* 3.1 25.9 + - - +
190B LEU* 3.7 29.6 - - + +
191B LEU* 3.9 23.3 - - + -
194B HIS* 3.7 43.1 - - + +
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Residues in contact with LYS 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 TYR* 3.1 49.1 + - + +
53B ASN* 2.7 38.9 + - - +
54B GLU 4.4 0.3 - - - +
55B ILE* 1.3 81.5 - - - +
57B ILE* 1.3 74.5 + - - +
58B SER* 3.4 2.0 + - - +
96B ALA 4.2 0.4 - - - -
98B LYS* 3.2 17.5 + - - -
186B LYS* 4.8 7.6 - - - +
190B LEU* 3.5 26.7 - - + -
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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