Contacts of the helix formed by residues 31 - 46 (chain A) in PDB entry 4LT6
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 LYS 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER 5.2 0.4 - - - +
30A PRO* 1.3 78.5 - - - +
32A GLU* 1.3 79.2 + - - +
33A ILE* 3.0 9.2 + - + +
34A ASP* 2.7 21.6 + - - +
35A HIS* 3.3 16.7 + - - -
329B SER* 5.8 1.1 - - - -
330B THR* 3.0 34.6 + - - +
402B GLY* 5.2 0.7 - - - +
405B GLU* 3.9 50.4 + - + +
406B ARG* 4.2 13.0 - - + +
411B THR 5.1 6.5 + - - -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 1.3 83.4 + - - +
33A ILE* 1.3 61.7 + - - +
35A HIS* 3.3 14.4 + - + +
36A ILE* 3.2 23.3 + - - +
309B TYR* 3.6 35.8 - - + +
311B LEU* 3.7 36.9 - - + +
330B THR* 3.4 20.6 + - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 4.5 6.0 - - + +
32A GLU* 1.3 77.4 - - - +
34A ASP* 1.3 72.2 + - - +
36A ILE* 2.7 39.5 + - + +
37A TYR* 2.8 53.0 + - + +
326B TYR 4.5 15.9 - - - +
327B ASN* 5.6 4.9 - - - +
398B ARG* 5.9 4.5 - - - +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 3.4 20.7 - - + +
31A LYS* 2.7 31.7 + - - +
33A ILE* 1.3 86.0 - - - +
35A HIS* 1.3 61.0 + - - +
37A TYR* 4.2 14.0 - - - -
38A THR* 3.0 27.6 + - - -
263A ALA* 4.5 7.2 - - + -
265A SER* 3.2 7.5 + - - +
266A THR* 4.1 11.0 + - - +
351A LEU* 5.6 4.0 - - - +
406B ARG* 3.5 27.9 + - - +
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 3.8 32.5 + - + +
31A LYS 3.3 21.7 + - - -
32A GLU* 3.3 10.9 + - + +
33A ILE 3.1 0.6 - - - -
34A ASP* 1.3 78.3 - - - +
36A ILE* 1.3 63.3 + - - +
38A THR* 3.4 8.0 + - - -
39A GLN* 3.1 22.3 + - - +
263A ALA* 5.1 6.0 - - + +
309B TYR* 3.8 40.7 + + + +
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU 3.2 13.9 + - - +
33A ILE* 2.7 26.7 + - + +
35A HIS* 1.3 79.1 - - - +
37A TYR* 1.3 58.6 + - + +
39A GLN* 3.3 4.3 + - - +
40A LYS* 3.1 44.6 + - + +
306B SER* 3.7 27.9 - - - +
309B TYR* 3.4 21.3 - - + +
310B HIS* 3.4 36.8 - - + +
326B TYR 6.2 0.2 - - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 2.8 57.0 + - + +
34A ASP* 3.7 11.9 - - - +
35A HIS 3.3 0.2 - - - -
36A ILE* 1.3 79.2 - - + +
38A THR* 1.3 60.4 + - - +
40A LYS* 3.4 12.8 + - + -
41A LEU* 2.9 11.4 + - - +
265A SER* 3.7 17.7 - - - -
350A ILE* 3.5 25.1 - - + -
351A LEU* 3.4 40.2 + - + -
352A GLN* 3.4 3.3 - - - -
353A GLY* 3.2 26.9 + - - -
357A TRP* 2.9 30.0 + + - +
398B ARG* 5.5 1.0 + - - -
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 3.0 11.4 + - - -
35A HIS* 3.7 9.0 - - - -
36A ILE 3.3 0.2 - - - -
37A TYR* 1.3 76.9 - - - +
39A GLN* 1.3 62.8 + - - +
41A LEU* 3.0 8.4 + - + +
42A ILE* 2.9 25.5 + - + +
221A LEU* 3.7 27.8 - - + -
263A ALA* 3.4 12.8 - - + +
264A ALA* 4.2 9.9 - - + +
265A SER* 2.7 28.0 + - - -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS 3.1 14.6 + - - +
36A ILE 3.3 7.1 + - - +
38A THR* 1.3 76.4 - - - +
40A LYS* 1.3 56.3 + - - +
42A ILE* 3.2 21.4 + - - +
43A ASP* 2.9 64.0 + - - +
46A LYS* 4.9 3.6 - - - +
305B PRO* 4.1 26.4 - - + +
306B SER* 3.8 30.1 - - - +
308B ARG* 5.4 1.4 + - - -
309B TYR* 6.0 2.8 - - + -
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 3.1 29.1 + - + +
37A TYR* 3.6 16.2 - - + +
39A GLN* 1.3 76.5 - - - +
41A LEU* 1.3 52.8 + - - +
43A ASP* 3.6 10.5 - - + +
44A ALA* 2.8 36.4 + - - +
356A ASP* 4.9 15.8 + - - +
357A TRP* 3.4 20.0 - - + +
306B SER* 4.6 14.1 - - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR 2.9 14.0 + - - +
38A THR* 3.0 10.7 + - - +
40A LYS* 1.3 73.4 - - - +
42A ILE* 1.3 66.4 + - - +
44A ALA* 3.3 2.5 + - + +
45A MET* 3.0 53.4 + - + +
221A LEU* 4.8 4.0 - - + +
225A ALA* 3.9 21.3 - - + -
264A ALA* 4.4 18.8 - - + -
265A SER 4.6 5.2 - - - +
268A VAL* 4.0 14.6 - - + -
357A TRP* 3.3 42.8 - - + +
360A LEU* 6.0 1.6 - - + -
361A LEU* 5.7 5.2 - - + -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 2.9 17.1 + - + +
39A GLN* 3.6 22.0 - - - +
41A LEU* 1.3 75.0 - - - +
43A ASP* 1.3 59.4 + - - +
45A MET* 3.2 9.6 + - + +
46A LYS* 3.1 46.3 + - - +
51A PHE* 4.0 20.4 - - + -
221A LEU* 3.8 35.2 - - + -
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 2.9 50.2 + - - +
40A LYS* 3.7 10.5 - - + +
41A LEU 3.1 0.4 - - - -
42A ILE* 1.3 75.8 - - - +
44A ALA* 1.3 65.0 + - - +
46A LYS* 3.5 22.0 + - - +
47A PRO* 3.2 18.2 - - - +
305B PRO* 5.4 3.9 - - - +
306B SER* 5.5 0.9 + - - -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS 2.8 20.1 + - - +
41A LEU* 3.7 4.0 - - + +
43A ASP* 1.3 73.2 - - - +
45A MET* 1.3 60.9 + - - +
47A PRO* 3.3 16.6 - - - +
48A PHE* 3.5 16.1 - - + -
357A TRP* 3.6 26.0 - - + -
358A SER* 4.6 8.7 - - - +
361A LEU* 4.5 12.1 - - + -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.0 55.1 + - + +
42A ILE* 3.6 7.6 - - - +
43A ASP 3.2 0.6 - - - -
44A ALA* 1.3 78.3 - - - +
46A LYS* 1.3 65.9 + - - +
48A PHE* 3.0 20.3 + - - +
50A VAL* 3.6 14.5 - - + +
51A PHE* 4.1 12.6 - - + -
221A LEU* 3.6 28.0 - - + -
224A ARG* 4.1 11.7 - - - +
225A ALA* 3.6 30.3 - - + -
228A LEU* 3.8 23.6 - - + -
361A LEU* 5.1 3.1 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 4.9 3.6 - - - +
42A ILE* 3.1 28.4 + - - +
43A ASP* 3.5 25.1 + - - +
45A MET* 1.3 75.4 - - - +
47A PRO* 1.3 69.9 - - + +
48A PHE 2.9 1.4 + - - -
49A GLY* 3.1 13.5 + - - -
50A VAL 4.4 0.7 + - - -
51A PHE* 4.0 26.3 + - + -
109A LYS* 5.9 0.9 + - - -
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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
------------------------------------------------------------
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