Contacts of the helix formed by residues 32 - 49 (chain D) in PDB entry 4LL4
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C GLU* 4.1 0.2 - - - -
247C CYS* 2.2 51.8 - - + -
29D ALA* 3.8 14.5 - - + +
30D THR 3.6 0.8 - - - -
31D TRP* 1.3 79.7 - - + +
33D GLY* 1.3 67.7 + - - +
34D PRO* 3.2 15.5 - - - -
35D ALA* 3.3 25.5 - - + +
36D LYS* 2.7 25.4 + - - +
74D MET* 3.7 12.1 - - + -
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Residues in contact with GLY 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLU* 3.4 20.8 + - - -
204C THR* 5.3 2.5 - - - -
31D TRP 3.6 2.6 + - - -
32D CYS* 1.3 71.9 - - - +
34D PRO* 1.3 60.9 - - - +
36D LYS* 2.9 17.5 + - - +
37D MET* 2.7 35.0 + - - +
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Residues in contact with PRO 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLU* 4.0 8.5 - - + +
204C THR* 4.1 17.0 - - + -
245C GLY* 3.3 23.8 - - - +
246C THR* 3.6 22.9 - - - +
247C CYS* 3.5 6.5 - - - -
32D CYS* 3.2 17.5 - - - -
33D GLY* 1.3 89.3 - - - +
35D ALA* 1.3 62.7 + - - +
37D MET* 3.1 15.9 + - + +
38D ILE* 3.2 10.7 + - - +
75D PRO* 3.8 5.6 - - + -
92D ALA* 3.6 19.7 - - + +
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 5.3 0.8 - - - +
28D SER* 3.5 23.1 - - - +
29D ALA 3.8 10.3 - - - +
32D CYS* 3.1 27.7 + - + -
34D PRO* 1.3 80.2 - - - +
36D LYS* 1.3 62.0 + - - +
38D ILE* 3.5 3.7 - - - +
39D LYS* 3.4 26.3 + - - +
74D MET* 4.7 0.9 - - + -
75D PRO* 3.6 24.5 - - + +
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Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ALA 4.9 2.1 + - - +
30D THR* 4.1 24.0 - - - +
31D TRP* 4.2 9.3 + - - +
32D CYS 2.7 24.5 + - - +
33D GLY* 3.2 17.0 - - - +
35D ALA* 1.3 69.4 - - - +
37D MET* 1.3 67.9 + - - +
39D LYS* 3.4 18.5 + - + +
40D PRO* 3.5 9.0 - - - +
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Residues in contact with MET 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLY 2.7 16.3 + - - +
34D PRO* 3.1 10.0 + - + +
36D LYS* 1.3 72.7 - - - +
38D ILE* 1.3 64.6 + - - +
40D PRO* 3.1 21.3 - - - +
41D PHE* 4.0 24.5 - - + -
92D ALA* 3.6 35.2 - - + +
94D LYS* 5.2 8.3 - - + -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 4.9 5.6 - - - +
34D PRO 3.2 9.7 + - - +
35D ALA* 3.5 12.6 - - - +
37D MET* 1.3 82.1 - - - +
39D LYS* 1.3 62.1 + - - +
40D PRO 3.4 0.7 - - - -
41D PHE* 2.9 13.5 + - + -
42D PHE* 2.7 28.3 + - + +
75D PRO* 4.3 10.3 - - + -
77D PHE* 4.2 23.8 - - + -
92D ALA* 3.5 10.8 - - + -
93D ASN 3.3 32.3 - - - +
94D LYS* 3.7 19.5 - - + +
97D LEU* 4.3 20.0 - - + -
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLN* 5.5 2.0 + - - -
26D ASP* 4.3 12.3 - - - +
28D SER* 4.6 7.4 - - - +
35D ALA 3.4 15.0 - - - +
36D LYS* 3.4 11.8 + - + +
37D MET 3.2 0.4 - - - -
38D ILE* 1.3 77.3 - - - +
40D PRO* 1.3 72.2 - - + +
42D PHE* 3.0 17.4 + - + +
43D HIS* 3.0 13.1 + - - +
56D GLU* 3.4 26.7 + - - +
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Residues in contact with PRO 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LYS 3.5 7.0 - - - +
37D MET 3.1 16.6 - - - +
38D ILE 3.6 0.2 - - - -
39D LYS* 1.3 96.0 - - + +
41D PHE* 1.3 66.4 + - + +
43D HIS* 3.2 9.2 + - + +
44D SER* 2.9 32.7 + - - +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D MET* 4.0 30.3 - - + -
38D ILE* 2.9 14.7 + - + +
40D PRO* 1.3 82.3 - - + +
42D PHE* 1.3 67.7 + - - +
43D HIS 3.0 0.5 + - - -
44D SER* 3.2 10.8 + - - +
45D LEU* 3.1 32.2 + - + +
94D LYS* 3.4 50.5 - - + -
97D LEU* 5.2 0.9 - - + -
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D VAL* 3.5 34.8 - - + -
24D VAL* 3.6 28.0 - - + -
26D ASP* 3.6 25.6 - - + +
38D ILE* 2.7 13.8 + - + +
39D LYS* 3.0 12.1 + - + +
41D PHE* 1.3 78.1 - - - +
43D HIS* 1.3 56.0 + - - +
45D LEU* 3.3 7.1 - - + +
46D SER* 3.1 24.9 + - - -
54D PHE* 3.9 19.6 - + + -
55D LEU 3.3 27.1 - - - -
56D GLU* 5.5 1.1 - - + -
77D PHE* 3.5 30.1 - + + -
97D LEU* 4.1 16.4 - - + -
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Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.5 47.6 - - + +
2D VAL* 4.1 13.7 + - + +
39D LYS 3.0 8.8 + - - +
40D PRO* 3.3 12.1 - - + +
41D PHE 3.0 0.2 - - - -
42D PHE* 1.3 79.7 - - - +
44D SER* 1.3 69.9 + - - +
46D SER* 2.9 25.3 + - - -
47D GLU* 3.2 18.0 + - + +
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PRO* 2.9 22.7 + - - +
41D PHE* 3.8 13.4 - - - -
43D HIS* 1.3 79.4 - - - +
45D LEU* 1.3 55.0 + - - +
47D GLU* 3.1 9.4 + - - +
48D LYS* 2.8 33.8 + - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.1 14.1 + - + +
42D PHE* 3.3 9.9 - - - +
44D SER* 1.3 80.1 - - - +
46D SER* 1.3 56.0 + - - +
48D LYS* 2.9 6.6 + - + +
49D TYR* 2.7 56.6 + - + -
54D PHE* 3.7 11.3 - - + -
94D LYS* 5.0 2.9 - - + +
97D LEU* 3.4 39.9 - - + -
98D GLU* 4.1 25.1 - - + +
101D ILE* 4.2 16.4 - - + -
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Residues in contact with SER 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.6 52.2 + - - -
2D VAL* 3.7 3.7 + - - +
42D PHE 3.1 11.6 + - - -
43D HIS 2.9 15.6 + - - -
45D LEU* 1.3 76.8 - - - +
47D GLU* 1.3 61.4 + - - +
49D TYR 3.8 13.3 - - - +
50D SER* 4.0 5.7 + - - -
54D PHE* 3.4 35.2 - - - -
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.8 41.0 + - - +
43D HIS* 3.2 24.1 + - + +
44D SER* 3.1 10.1 + - - +
46D SER* 1.3 82.0 + - - +
48D LYS* 1.3 64.6 + - - +
50D SER* 4.1 10.2 + - - -
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Residues in contact with LYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER 2.8 17.8 + - - +
45D LEU* 2.9 9.9 + - + +
47D GLU* 1.3 76.8 - - - +
49D TYR* 1.3 100.3 + - + +
50D SER* 2.9 10.7 + - - -
98D GLU* 3.9 7.4 - - - +
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 2.7 41.9 + - + +
46D SER 3.8 3.1 - - - -
48D LYS* 1.3 98.9 - - + +
50D SER* 1.3 55.8 + - - +
51D ASN* 2.9 21.7 + - - +
52D VAL* 3.0 35.7 + - + +
54D PHE* 3.5 10.5 - - + -
98D GLU* 2.4 34.7 + - + -
101D ILE* 4.2 18.8 - - + -
102D ASN* 3.2 30.9 + - - -
105D VAL* 5.3 4.0 - - + -
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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