Contacts of the helix formed by residues 35 - 56 (chain D) in PDB entry 4K71
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 PRO 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D GLN 3.8 6.5 - - - +
34D CYS* 1.4 88.1 - - - +
36D PHE* 1.3 65.6 + - - +
37D GLU* 4.1 13.5 - - + +
38D ASP* 3.0 32.9 + - - +
39D HIS* 3.3 9.2 + - - +
83D THR* 5.7 1.6 - - + -
84D TYR* 3.6 13.0 - - - +
140D TYR* 3.4 5.4 - - - +
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.5 4.7 - - + -
35D PRO* 1.3 70.4 - - - +
37D GLU* 1.3 86.7 + - + +
38D ASP 3.2 0.2 + - - -
39D HIS* 3.2 2.2 + - - +
40D VAL* 3.0 53.9 + - + +
133D THR* 3.8 30.1 - - + -
136D LYS* 3.7 13.9 - - + -
137D LYS* 3.5 52.9 - - + +
140D TYR* 3.3 51.4 + + + -
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PRO* 3.2 10.6 + - + +
36D PHE* 1.3 95.2 + - + +
38D ASP* 1.3 65.5 + - - +
40D VAL* 3.6 4.7 + - - +
41D LYS* 3.4 20.8 + - - +
137D LYS* 3.5 22.3 + - - -
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Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D CYS* 3.6 13.7 - - - -
35D PRO* 3.0 31.2 + - - +
37D GLU* 1.3 78.1 - - - +
39D HIS* 1.3 64.8 + - - +
41D LYS* 3.5 17.3 + - + +
42D LEU* 3.3 27.9 + - + +
77D VAL* 4.4 20.7 - - + +
84D TYR* 5.1 0.2 + - - -
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Residues in contact with HIS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.0 15.0 - - + -
27D PHE* 3.2 38.4 + + + -
28D ALA* 3.6 17.1 - - - +
31D LEU* 3.1 30.7 + - + +
34D CYS* 3.5 29.6 + - + +
35D PRO 3.3 1.4 + - - +
36D PHE* 3.2 8.9 + - - +
38D ASP* 1.3 80.3 - - - +
40D VAL* 1.3 57.6 + - - +
42D LEU* 3.2 9.7 + - + +
43D VAL* 2.9 31.8 + - - +
74D LEU* 5.0 4.5 - - + -
140D TYR* 3.2 24.9 - + - -
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.7 7.6 - - + -
36D PHE* 3.0 58.2 + - + +
37D GLU* 4.0 5.6 - - - +
38D ASP 3.3 0.2 - - - -
39D HIS* 1.3 72.2 - - - +
41D LYS* 1.3 57.3 + - - +
43D VAL* 3.1 8.6 + - + +
44D ASN* 2.8 54.0 + - - +
133D THR* 6.5 0.2 - - + -
136D LYS* 5.0 14.8 - - + +
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Residues in contact with LYS 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 GLU 3.4 11.2 + - - +
38D ASP* 3.5 22.8 + - + +
40D VAL* 1.3 78.8 - - - +
42D LEU* 1.3 78.7 + - + +
44D ASN* 3.1 9.5 + - - +
45D GLU* 3.0 50.8 + - - +
76D THR* 4.4 12.3 + - - +
77D VAL* 5.7 5.9 - - - +
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Residues in contact with LEU 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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27D PHE* 3.8 16.8 - - + -
31D LEU* 5.9 0.2 - - + -
34D CYS* 5.6 2.2 - - - -
38D ASP* 3.3 15.7 - - + +
39D HIS* 3.2 15.4 + - + +
41D LYS* 1.3 95.1 - - - +
43D VAL* 1.3 61.6 + - - +
45D GLU* 3.3 19.8 + - - +
46D VAL* 3.2 27.2 + - - +
73D LYS* 3.4 36.9 - - + +
74D LEU* 4.2 15.5 - - + +
76D THR* 3.7 20.2 - - + +
77D VAL* 5.2 9.6 - - + -
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS* 3.8 26.9 - - + +
23D VAL* 3.7 7.9 - - + +
24D LEU* 3.5 33.9 - - + +
27D PHE* 3.4 24.9 - - + -
39D HIS 2.9 17.4 + - - +
40D VAL* 3.5 11.0 - - + +
42D LEU* 1.3 78.1 - - - +
44D ASN* 1.3 63.6 + - - +
46D VAL* 3.4 2.9 + - - +
47D THR* 2.9 39.1 + - - +
136D LYS* 6.3 2.5 - - + +
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS* 3.3 25.8 + - - +
40D VAL* 2.8 41.0 + - - +
41D LYS* 3.1 7.1 + - - +
43D VAL* 1.3 77.2 - - - +
45D GLU* 1.3 58.4 + - + +
47D THR* 3.5 7.4 + - - +
48D GLU* 2.9 28.5 + - - +
136D LYS* 4.5 6.6 + - - +
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Residues in contact with GLU 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 LYS* 3.0 47.8 + - - +
42D LEU* 3.6 15.5 - - - +
43D VAL 3.2 0.2 - - - -
44D ASN* 1.3 76.1 - - + +
46D VAL* 1.3 60.4 + - - +
48D GLU* 3.3 14.4 + - - +
49D PHE* 3.0 28.6 + - - +
73D LYS* 2.5 43.4 + - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 5.0 0.4 - - + -
19D PHE* 4.3 15.7 - - + -
23D VAL* 4.3 10.1 - - + -
27D PHE* 4.1 14.1 - - + -
42D LEU 3.2 12.9 + - - +
43D VAL 3.7 7.2 - - - +
45D GLU* 1.3 76.4 - - - +
47D THR* 1.3 57.5 + - - +
49D PHE* 3.4 7.5 + - - +
50D ALA* 2.9 27.0 + - - +
69D LEU* 4.1 23.6 - - + -
70D PHE* 3.8 24.0 - - + -
73D LYS* 3.7 25.8 - - + +
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Residues in contact with THR 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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11D PHE* 4.4 5.8 - - + -
16D GLU* 4.2 16.2 - - + +
19D PHE* 3.8 16.4 - - - -
20D LYS* 3.4 48.0 - - + +
23D VAL* 5.6 0.5 - - - +
43D VAL* 2.9 20.0 + - - +
44D ASN 3.5 6.5 - - - +
46D VAL* 1.3 73.4 - - - +
48D GLU* 1.3 64.5 + - - +
50D ALA* 3.3 2.4 + - - +
51D LYS* 3.2 32.0 + - - +
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Residues in contact with GLU 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 ASN 2.9 17.2 + - - +
45D GLU* 3.3 15.7 + - - +
47D THR* 1.3 76.2 - - - +
49D PHE* 1.3 62.3 + - - +
51D LYS* 3.4 12.2 + - - +
52D THR* 3.3 24.3 + - - +
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Residues in contact with PHE 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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7D VAL* 4.0 9.2 - - + -
45D GLU 3.0 17.3 + - - +
46D VAL* 3.6 4.7 - - - +
47D THR 3.3 0.2 - - - -
48D GLU* 1.3 75.1 - - - +
50D ALA* 1.3 67.8 + - - +
52D THR* 3.1 23.0 + - + -
53D CYS* 3.1 36.1 + - - -
60D GLU 3.6 18.2 - - - -
61D ASN* 3.4 33.0 - - + -
62D CYS* 3.9 1.3 - - - -
64D LYS* 6.1 1.6 - - + -
69D LEU* 3.6 40.2 - - + -
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Residues in contact with ALA 50 (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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7D VAL* 3.7 21.8 - - + +
8D ALA* 4.6 0.5 - - - -
11D PHE* 3.8 17.0 - - + -
19D PHE* 3.6 26.5 - - + -
46D VAL 2.9 17.9 + - - +
47D THR 3.3 5.8 + - - +
49D PHE* 1.3 74.9 - - - +
51D LYS* 1.3 50.9 + - - +
53D CYS* 3.0 6.1 + - - +
54D VAL* 2.8 38.4 + - - +
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Residues in contact with LYS 51 (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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11D PHE* 3.8 20.6 - - + -
16D GLU* 3.1 41.8 + - - -
47D THR* 3.2 19.3 + - + +
48D GLU* 3.6 11.7 - - - +
49D PHE 3.2 0.8 - - - -
50D ALA* 1.3 73.6 - - - +
52D THR* 1.3 60.9 + - - +
54D VAL* 3.7 8.7 - - - +
55D ALA* 3.0 29.5 + - - +
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Residues in contact with THR 52 (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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48D GLU* 3.3 14.8 + - - +
49D PHE* 3.1 17.9 + - + -
51D LYS* 1.3 78.0 - - - +
53D CYS* 1.3 59.5 + - - +
55D ALA* 3.6 4.3 + - - +
56D ASP* 3.1 27.3 + - + +
59D ALA* 3.9 21.5 - - + -
62D CYS* 4.9 2.5 - - - -
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Residues in contact with CYS 53 (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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5D SER* 3.7 16.4 - - - +
7D VAL* 4.0 6.3 - - + -
8D ALA* 4.0 7.2 - - + -
49D PHE* 3.4 31.2 - - - -
50D ALA 3.0 7.9 + - - +
52D THR* 1.3 75.0 - - - +
54D VAL* 1.3 65.4 + - - +
56D ASP 3.6 1.6 - - - -
57D GLU* 3.0 30.7 + - - +
62D CYS* 2.1 54.3 - - + -
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Residues in contact with VAL 54 (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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8D ALA* 3.9 25.8 - - + +
11D PHE* 3.6 33.0 - - + -
12D LYS* 4.2 27.7 + - + +
50D ALA 2.8 19.1 + - - +
51D LYS* 3.7 8.5 - - - +
53D CYS* 1.3 78.3 - - - +
55D ALA* 1.3 62.8 + - - +
56D ASP* 3.3 0.9 + - - -
57D GLU* 4.9 4.0 + - - +
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Residues in contact with ALA 55 (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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51D LYS 3.0 17.8 + - - +
52D THR* 4.0 5.2 - - - +
54D VAL* 1.3 79.4 - - + +
56D ASP* 1.3 62.5 + - + +
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Residues in contact with ASP 56 (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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52D THR* 3.1 19.1 + - + +
53D CYS* 3.1 6.0 - - - +
54D VAL 3.2 1.4 - - - -
55D ALA* 1.3 82.1 - - + +
57D GLU* 1.3 58.4 + - - +
58D SER* 2.6 33.9 + - - -
59D ALA* 3.2 26.5 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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