Contacts of the helix formed by residues 32 - 49 (chain B) in PDB entry 4LL1
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 CYS 32 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 3.8 0.2 - - - -
247A CYS* 2.7 48.0 - - + -
29B ALA* 3.6 20.4 - - + +
30B THR 3.4 1.6 - - - -
31B TRP* 1.3 82.2 - - + +
33B GLY* 1.3 64.7 + - - +
34B PRO* 3.9 2.2 - - - -
35B ALA* 3.2 26.8 + - + +
36B LYS* 3.0 26.2 + - - +
74B MET* 3.7 15.7 - - + -
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 2.7 23.5 + - - -
204A THR* 5.2 3.1 - - - -
31B TRP 3.5 0.8 + - - -
32B CYS* 1.3 70.7 - - - +
34B PRO* 1.4 69.7 - - - +
36B LYS* 3.3 7.9 + - - +
37B MET* 3.0 23.4 + - - +
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 4.0 3.1 - - + +
203A ASN 4.5 0.2 - - - +
204A THR* 3.8 27.8 - - + -
245A GLY* 3.3 38.8 - - - +
246A THR 3.9 5.2 - - - +
247A CYS* 3.7 20.0 - - - -
33B GLY* 1.4 86.4 - - - +
35B ALA* 1.3 59.0 + - - +
37B MET* 3.4 8.3 + - + +
38B ILE* 3.1 18.2 + - - +
75B PRO* 4.0 5.6 - - + -
92B ALA* 3.2 22.8 - - + +
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.9 1.4 - - - +
28B SER* 3.4 28.4 + - - +
29B ALA 3.8 9.6 - - - +
32B CYS* 3.2 26.7 + - + +
34B PRO* 1.3 77.0 - - - +
36B LYS* 1.3 61.3 + - - +
38B ILE* 3.3 16.7 - - - +
39B LYS* 3.3 11.3 + - - +
74B MET* 4.7 0.2 - - + -
75B PRO* 3.8 23.8 - - + +
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 4.6 2.2 - - - +
30B THR* 3.4 33.1 + - - +
31B TRP 5.2 1.1 - - - -
32B CYS 3.0 21.0 + - - +
33B GLY* 3.6 6.3 - - - +
35B ALA* 1.3 74.4 - - - +
37B MET* 1.3 64.9 + - - +
38B ILE 3.3 0.2 - - - -
39B LYS* 3.5 32.0 - - + +
40B PRO* 3.5 6.4 - - - +
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLY 3.0 17.2 + - - +
34B PRO* 3.7 6.1 - - + +
35B ALA 3.4 0.2 - - - -
36B LYS* 1.3 76.5 - - - +
38B ILE* 1.3 69.7 + - - +
40B PRO* 3.2 13.4 - - - +
41B PHE* 3.4 26.5 - - + -
92B ALA* 3.4 39.3 - - + +
94B LYS* 5.0 3.6 - - + -
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Residues in contact with ILE 38 (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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26B ASP* 4.3 7.0 - - - +
34B PRO 3.1 15.3 + - - +
35B ALA* 3.3 15.7 - - - +
37B MET* 1.3 77.7 - - - +
39B LYS* 1.3 66.7 + - - +
40B PRO 3.4 0.4 - - - -
41B PHE* 2.9 19.5 + - + +
42B PHE* 3.0 11.7 + - + +
75B PRO* 3.8 18.8 - - + -
77B PHE* 3.9 25.4 - - + -
92B ALA* 3.8 27.6 - - + +
93B ASN 4.1 1.8 - - - +
94B LYS* 3.6 40.2 - - + +
97B LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.8 4.3 - - - +
28B SER* 6.1 0.4 - - - +
35B ALA 3.3 14.6 + - - +
36B LYS* 3.5 25.6 - - + +
38B ILE* 1.3 79.7 - - - +
40B PRO* 1.4 87.0 - - + +
41B PHE 3.2 0.2 + - - -
42B PHE* 3.3 8.5 + - - +
43B HIS* 3.3 18.3 + - - +
56B GLU* 4.6 20.0 - - - +
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Residues in contact with PRO 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS 3.5 7.0 - - - +
37B MET 3.2 16.4 - - - +
39B LYS* 1.4 108.6 - - + +
41B PHE* 1.3 60.1 + - + +
43B HIS* 3.0 10.5 + - + +
44B SER* 2.8 38.4 + - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 3.4 37.0 - - + -
38B ILE* 2.9 14.6 + - + +
40B PRO* 1.3 84.0 - - + +
42B PHE* 1.3 57.8 + - - +
44B SER* 3.4 10.3 + - - -
45B LEU* 2.9 39.8 + - + +
94B LYS* 3.5 51.1 - - + -
97B LEU* 5.6 0.7 - - + -
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Residues in contact with PHE 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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2B VAL* 3.8 28.7 - - + -
24B VAL* 3.8 23.6 - - + -
26B ASP* 3.5 32.5 - - + +
38B ILE* 3.0 10.7 + - + +
39B LYS* 3.5 11.0 - - - +
40B PRO 3.2 0.2 - - - -
41B PHE* 1.3 78.7 - - - +
43B HIS* 1.3 58.8 + - - +
45B LEU* 3.6 5.6 + - - -
46B SER* 3.3 15.9 + - - -
54B PHE* 3.5 34.6 - + + -
55B LEU 3.5 22.0 - - - -
56B GLU* 4.9 4.9 - - + -
77B PHE* 3.6 26.7 - + + -
97B LEU* 3.9 14.7 - - + +
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.3 12.8 - - + +
2B VAL* 4.0 24.0 - - + -
39B LYS* 3.3 9.4 + - + +
40B PRO* 3.0 12.3 + - + +
42B PHE* 1.3 76.4 - - - +
44B SER* 1.3 68.5 + - - +
45B LEU 3.2 1.3 - - - -
46B SER* 2.4 32.6 + - - -
47B GLU* 3.2 40.3 + - + +
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Residues in contact with SER 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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40B PRO* 2.8 22.0 + - - +
41B PHE* 3.7 12.2 - - - -
43B HIS* 1.3 75.7 + - - +
45B LEU* 1.3 60.4 + - - +
47B GLU* 3.5 9.9 + - - +
48B LYS* 3.2 22.2 + - - +
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Residues in contact with LEU 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 PHE* 2.9 22.5 + - + +
42B PHE* 3.7 2.0 - - - +
43B HIS 3.2 0.2 - - - -
44B SER* 1.3 74.3 - - - +
46B SER* 1.3 57.9 + - - +
48B LYS* 4.4 2.9 - - + -
49B TYR* 2.8 57.6 + - + -
54B PHE* 3.4 23.4 - - + -
94B LYS* 4.8 4.0 - - + +
97B LEU* 3.5 39.3 - - + -
98B GLU* 3.6 30.7 - - + +
101B ILE* 4.3 7.4 - - + -
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Residues in contact with SER 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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1B MET* 3.4 35.2 + - - +
2B VAL* 3.6 7.2 - - - +
42B PHE 3.3 7.6 + - - -
43B HIS* 2.4 30.9 + - - -
45B LEU* 1.3 74.2 - - - +
47B GLU* 1.3 62.7 + - - +
49B TYR 3.9 12.5 - - - +
50B SER* 4.1 5.4 + - - -
52B VAL 5.0 0.7 - - - +
54B PHE* 3.5 34.5 - - - -
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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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1B MET* 2.8 44.0 + - - +
43B HIS* 3.2 38.0 + - + +
44B SER* 3.8 10.8 - - - +
46B SER* 1.3 75.6 - - - +
48B LYS* 1.3 68.5 + - - +
49B TYR 3.6 0.2 + - - -
50B SER* 4.0 10.4 + - - -
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Residues in contact with LYS 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 SER 3.2 14.3 + - - +
45B LEU* 3.4 6.7 + - + +
47B GLU* 1.3 82.0 - - - +
49B TYR* 1.3 97.1 + - + +
50B SER* 3.2 8.3 + - - -
51B ASN* 4.9 0.2 - - - +
98B GLU* 4.1 6.7 - - - +
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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 LEU* 2.8 43.7 + - + +
46B SER 3.9 4.6 - - - +
48B LYS* 1.3 98.9 + - + +
50B SER* 1.3 53.9 + - - +
51B ASN* 3.2 24.7 - - - +
52B VAL* 3.0 32.5 + - + +
54B PHE* 3.7 13.7 - + + -
98B GLU* 2.6 34.2 + - + -
101B ILE* 4.2 16.8 - - + -
102B ASN* 2.9 31.3 + - - -
105B VAL* 5.4 2.2 - - + -
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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