Contacts of the helix formed by residues 33 - 47 (chain B) in PDB entry 4J6V
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 GLY 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.6 2.8 - - - -
258A PHE* 3.6 24.3 - - - -
29B LEU 3.4 0.2 + - - -
30B LYS 3.3 10.2 + - - -
31B GLU 3.3 5.0 - - - -
32B LYS* 1.3 77.5 - - - +
34B ILE* 1.3 61.6 + - - +
35B TYR 3.6 2.5 - - - -
36B ASP* 3.9 19.9 + - - +
37B ARG* 3.9 9.0 + - - +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 4.0 19.3 - - + -
29B LEU* 3.0 32.2 + - + +
32B LYS* 4.4 22.9 - - + -
33B GLY* 1.3 76.4 - - - +
35B TYR* 1.3 67.7 + - - +
36B ASP 3.2 2.2 - - - -
37B ARG* 3.0 31.6 + - - +
38B TYR* 3.5 11.4 - - + -
79B ASP* 3.7 32.8 - - - +
82B SER* 5.9 1.6 - - - +
83B ILE* 5.7 2.2 - - + -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.0 19.3 - - + -
29B LEU* 3.1 11.6 + - + -
30B LYS* 3.6 39.0 - - + +
33B GLY 3.6 0.2 - - - -
34B ILE* 1.3 76.5 - - - +
36B ASP* 1.3 63.9 + - - +
38B TYR* 3.0 19.5 + - - +
39B ILE* 3.4 27.0 + - + -
76B PHE* 3.9 21.1 - + - -
136B TRP* 3.6 27.5 - + - -
222B PRO 2.6 29.7 + - - -
223B ASN* 4.6 0.4 - - - -
225B PRO* 3.5 20.4 - - + +
228B PHE* 3.3 28.1 - + - -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 4.0 15.0 - - + -
52A PRO* 4.2 21.1 - - + +
30B LYS* 4.2 21.0 + - - +
33B GLY* 3.9 18.4 + - - +
34B ILE 3.2 1.0 - - - -
35B TYR* 1.3 78.0 - - - +
37B ARG* 1.3 66.0 + - - +
39B ILE* 2.9 12.9 + - - +
40B ALA* 2.9 23.0 + - - +
139B ILE* 3.0 40.9 - - + +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.7 27.6 - - + -
258A PHE* 4.0 24.8 - - - -
265A PRO* 3.6 20.7 + - - +
267A TYR* 3.6 31.0 - - + +
269A TRP 3.2 19.2 + - - -
270A ASN* 2.9 31.7 - - - +
33B GLY 3.9 3.6 - - - +
34B ILE* 3.0 22.5 + - - +
36B ASP* 1.3 77.7 - - - +
38B TYR* 1.3 62.7 + - + +
40B ALA 3.4 0.2 + - - -
41B TRP* 2.9 62.0 + - + +
79B ASP* 5.9 0.4 + - - -
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.5 23.3 - - + -
35B TYR* 3.0 13.4 + - + +
37B ARG* 1.3 79.4 - - + +
39B ILE* 1.3 64.6 + - + +
41B TRP* 3.5 26.4 + + - -
42B HIS 3.2 14.4 + - - -
72B TYR* 2.6 57.4 + + + +
75B ARG* 3.0 25.3 + - + +
76B PHE* 3.6 41.3 - + + -
79B ASP* 2.6 29.9 + - - -
228B PHE* 4.1 11.2 - + + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 4.1 6.1 - - - +
35B TYR* 3.4 38.6 + - + +
36B ASP* 2.9 24.9 + - - +
38B TYR* 1.3 77.6 - - - +
40B ALA* 1.3 65.0 + - - +
42B HIS* 3.3 3.5 + - - +
43B GLY* 3.2 18.0 + - - -
139B ILE* 3.8 23.1 - - + +
140B ASP 5.7 1.3 - - - +
219B PRO 4.5 5.8 - - - +
220B THR* 5.1 3.6 - - - +
222B PRO* 4.0 21.5 - - + +
223B ASN* 3.5 35.9 - - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 5.8 0.4 - - - +
47A LYS 5.8 2.0 - - - +
48A PHE* 3.5 32.3 - - + -
267A TYR* 3.1 23.5 + - + +
36B ASP 2.9 10.7 + - - +
39B ILE* 1.3 76.8 - - - +
41B TRP* 1.3 53.7 + - - +
43B GLY* 3.2 3.3 + - - -
44B ALA* 2.8 32.4 + - - +
139B ILE* 5.1 4.9 - - + +
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Residues in contact with TRP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A TYR* 3.2 28.1 + + - -
268A PRO* 3.0 28.9 + - + +
269A TRP 5.1 0.7 - - - -
270A ASN* 4.3 5.6 - - - -
37B ARG* 2.9 55.1 + - - +
38B TYR* 3.8 45.3 - + - +
40B ALA* 1.3 73.2 - - - +
42B HIS* 1.3 57.2 - - - +
44B ALA* 3.2 3.7 + - - +
45B ALA* 3.0 29.3 + - - +
68B TRP* 4.0 4.0 - - - -
72B TYR* 4.3 7.0 - + + -
75B ARG* 3.9 22.9 - - - -
268B PRO* 3.5 27.8 - - + +
269B TRP* 3.6 34.8 - + + -
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR 3.2 10.5 + - - +
39B ILE 3.6 8.1 - - - +
40B ALA 3.2 0.4 - - - -
41B TRP* 1.3 80.5 - - - +
43B GLY* 1.3 61.9 + - - +
45B ALA* 3.4 4.0 + - - +
46B GLY* 3.4 15.9 + - - -
59B ALA* 5.1 0.2 - - + -
60B HIS* 3.1 17.8 + + - -
68B TRP* 3.9 28.0 - + - -
69B HIS* 3.9 2.0 - - - -
72B TYR* 3.9 4.0 - + + +
218B VAL* 2.9 33.7 + - + -
219B PRO* 3.3 13.0 + - + +
222B PRO* 3.7 15.1 - - + +
227B PHE* 3.8 17.7 - + - -
401B CU 1.9 31.5 - - - -
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Residues in contact with GLY 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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39B ILE 3.2 11.1 + - - -
40B ALA* 3.6 2.7 - - - -
42B HIS* 1.3 75.8 + - - +
44B ALA* 1.3 66.5 + - - +
46B GLY* 3.2 11.2 + - - -
47B LYS* 3.6 22.3 + - - +
141B GLU* 6.6 0.4 - - - -
219B PRO* 4.1 21.8 + - - +
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Residues in contact with ALA 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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40A ALA* 5.8 0.3 - - - +
44A ALA* 3.9 21.1 - - + -
267A TYR* 3.7 13.2 - - - +
268A PRO* 6.5 0.2 - - + -
40B ALA 2.8 20.2 + - - +
41B TRP* 3.2 6.5 + - - +
43B GLY* 1.3 72.9 - - - +
45B ALA* 1.3 62.5 + - - +
47B LYS* 3.1 26.9 + - - +
48B PHE 3.6 3.8 + - - -
267B TYR* 3.6 22.1 + - + +
268B PRO* 5.1 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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41B TRP 3.0 8.0 + - - +
42B HIS 3.7 5.2 - - - +
43B GLY 3.3 0.2 - - - -
44B ALA* 1.3 76.1 - - - +
46B GLY* 1.3 61.9 + - - +
48B PHE* 3.1 12.1 + - - +
57B ASN* 3.6 2.4 - - - +
58B ALA* 3.6 20.6 + - + -
59B ALA* 3.8 11.0 - - + -
68B TRP* 3.5 42.2 - - + +
267B TYR* 4.1 17.7 - - - +
268B PRO* 4.5 1.1 - - + +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS 3.4 7.3 + - - -
43B GLY* 3.2 9.1 + - - -
44B ALA 3.1 1.0 - - - -
45B ALA* 1.3 77.9 - - - +
47B LYS* 1.3 60.1 + - - +
48B PHE 3.4 1.1 + - - -
49B HIS* 3.6 21.8 + - - -
57B ASN* 3.8 20.7 + - - +
59B ALA* 5.4 0.4 - - - +
60B HIS* 5.1 4.9 - - - -
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Residues in contact with LYS 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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40A ALA* 5.5 4.8 - - + +
43A GLY 5.2 1.2 + - - -
44A ALA* 4.9 13.0 - - - +
47A LYS* 3.3 34.5 - - - +
141A GLU 4.2 13.5 - - - +
142A GLN* 4.0 39.7 - - - +
143A GLY* 3.6 22.6 - - - -
43B GLY 3.6 19.3 + - - +
44B ALA* 3.1 17.5 + - - +
46B GLY* 1.3 78.0 - - - +
48B PHE* 1.3 60.1 + - - +
49B HIS* 3.6 5.3 + - - -
141B GLU* 5.7 5.4 - - + +
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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