Contacts of the helix formed by residues 35 - 56 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLN 3.7 5.1 - - - +
34A CYS* 1.4 93.4 - - - +
36A PHE* 1.3 67.7 + - - +
37A GLU* 3.9 14.6 - - + +
38A ASP* 3.1 30.7 + - - +
39A HIS* 3.3 8.5 + - - +
83A THR* 5.9 2.5 - - + -
84A TYR* 3.4 12.8 - - - +
140A TYR* 3.6 4.0 - - - +
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.0 1.8 - - + -
35A PRO* 1.3 70.2 - - - +
37A GLU* 1.3 88.0 + - + +
39A HIS* 3.0 14.2 + - - +
40A VAL* 3.1 42.4 + - + +
133A THR* 3.9 22.7 - - + -
136A LYS* 3.7 12.8 - - + -
137A LYS* 3.6 56.5 - - + -
140A TYR* 3.3 49.0 + + + -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.9 11.5 - - + +
36A PHE* 1.3 107.6 + - + +
38A ASP* 1.3 65.9 + - - +
40A VAL* 3.6 5.5 + - - +
41A LYS* 3.1 23.4 + - - +
137A LYS* 4.9 5.9 + - - -
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 3.6 14.6 - - - -
35A PRO* 3.1 34.1 + - - +
37A GLU* 1.3 78.5 - - - +
39A HIS* 1.3 65.2 + - - +
41A LYS* 3.4 25.8 + - - +
42A LEU* 3.0 29.3 + - + +
77A VAL* 4.5 14.9 - - + +
84A TYR* 4.8 1.2 + - - -
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Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.0 14.4 - - + -
27A PHE* 3.3 37.5 + - + +
28A ALA* 3.6 16.4 - - + -
31A LEU* 3.1 33.6 + - + -
34A CYS* 3.4 28.1 - - + +
35A PRO 3.3 0.8 + - - -
36A PHE* 3.0 10.7 + - - +
38A ASP* 1.3 78.8 - - - +
40A VAL* 1.3 58.5 + - - +
42A LEU* 3.1 10.7 + - + +
43A VAL* 2.9 34.1 + - - +
74A LEU* 4.2 3.8 - - + -
140A TYR* 3.8 24.2 - + + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.8 8.5 - - + -
36A PHE* 3.1 52.8 + - + +
37A GLU* 3.9 7.0 - - - +
39A HIS* 1.3 71.8 - - - +
41A LYS* 1.3 64.8 + - - +
43A VAL* 3.2 8.5 + - - +
44A ASN* 2.9 46.9 + - - +
136A LYS* 4.5 23.1 - - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU 3.1 15.9 + - - +
38A ASP* 3.4 29.8 + - - +
40A VAL* 1.3 79.7 - - - +
42A LEU* 1.3 86.3 + - - +
44A ASN* 3.3 8.7 + - - +
45A GLU* 3.3 45.1 + - + +
76A THR* 5.2 2.2 + - - -
77A VAL* 4.6 11.7 - - - +
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Residues in contact with LEU 42 (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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27A PHE* 4.0 16.4 - - + -
34A CYS* 5.6 0.4 - - - -
38A ASP 3.0 20.0 + - - +
39A HIS* 3.1 21.1 + - + +
41A LYS* 1.3 96.9 - - - +
43A VAL* 1.3 61.4 + - - +
45A GLU* 3.3 16.5 + - - +
46A VAL* 3.1 26.3 + - - +
73A LYS* 3.5 35.2 - - + +
74A LEU* 4.4 12.8 - - + +
76A THR* 3.8 19.5 - - + +
77A VAL* 5.2 12.1 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.6 35.9 - - + +
23A VAL* 3.8 7.6 - - + -
24A LEU* 3.6 37.7 - - + +
27A PHE* 3.6 18.2 - - + -
39A HIS 2.9 21.7 + - - +
40A VAL* 3.2 8.3 + - - +
42A LEU* 1.3 71.6 - - - +
44A ASN* 1.3 61.5 + - - +
46A VAL* 3.4 2.6 + - - +
47A THR* 2.8 42.0 + - - +
136A LYS* 6.5 0.9 - - - -
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.6 26.5 + - - +
40A VAL* 2.9 38.3 + - - +
41A LYS* 3.6 7.8 - - - +
43A VAL* 1.3 78.2 - - - +
45A GLU* 1.3 57.5 + - + +
47A THR* 3.4 7.1 + - - +
48A GLU* 2.8 42.2 + - - +
136A LYS* 4.6 5.4 + - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.3 40.0 + - + +
42A LEU* 3.7 11.6 - - - +
43A VAL 3.2 0.8 - - - -
44A ASN* 1.3 74.5 - - + +
46A VAL* 1.3 67.0 + - - +
47A THR 3.2 0.2 - - - -
48A GLU* 3.2 21.3 + - - +
49A PHE* 2.9 23.0 + - - +
73A LYS* 2.5 44.8 + - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.0 6.4 - - + +
19A PHE* 4.1 22.7 - - + -
23A VAL* 4.3 14.8 - - + -
27A PHE* 3.8 22.7 - - + -
42A LEU 3.1 13.4 + - - +
43A VAL 3.6 7.6 - - - +
45A GLU* 1.3 76.7 - - - +
47A THR* 1.3 56.2 + - - +
49A PHE* 3.2 9.2 + - - +
50A ALA* 2.8 25.8 + - - +
69A LEU* 5.2 8.7 - - + +
70A PHE* 4.3 15.7 - - + -
73A LYS* 3.9 19.0 - - + +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.3 11.9 - - + -
16A GLU* 4.3 2.0 - - - +
19A PHE* 3.8 16.1 - - - -
20A LYS* 3.4 40.1 - - + +
43A VAL* 2.8 24.0 + - - +
44A ASN* 3.5 7.9 - - - +
45A GLU 3.2 0.2 - - - -
46A VAL* 1.3 73.7 - - - +
48A GLU* 1.3 66.0 + - + +
50A ALA* 3.1 2.3 + - - +
51A LYS* 3.0 45.9 + - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 2.8 36.8 + - - +
45A GLU* 3.2 19.6 + - - +
47A THR* 1.3 72.7 - - + +
49A PHE* 1.3 61.7 + - - +
51A LYS* 3.5 10.7 + - - +
52A THR* 3.1 25.2 + - - -
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 6.5 - - + -
45A GLU 2.9 12.9 + - - +
46A VAL* 3.5 11.7 - - - +
47A THR 3.1 0.2 - - - -
48A GLU* 1.3 76.0 - - - +
50A ALA* 1.3 65.5 + - - +
52A THR* 3.5 11.5 + - + -
53A CYS* 3.2 46.7 + - - -
59A ALA* 5.9 0.4 - - + -
60A GLU 3.5 15.7 - - - -
61A ASN* 3.5 35.9 - - + -
62A CYS* 4.1 1.6 - - - -
69A LEU* 3.5 38.6 - - + -
73A LYS* 6.5 0.4 - - - -
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Residues in contact with ALA 50 (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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7A VAL* 4.0 18.6 - - + +
8A ALA* 4.8 0.3 - - - -
11A PHE* 3.8 19.7 - - + -
19A PHE* 3.7 26.7 - - + -
46A VAL 2.8 13.7 + - - +
47A THR 3.1 7.4 + - - +
49A PHE* 1.3 77.6 - - - +
51A LYS* 1.3 56.9 + - - +
53A CYS* 3.1 4.0 + - - +
54A VAL* 2.9 33.1 + - - +
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Residues in contact with LYS 51 (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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11A PHE* 3.8 18.8 - - + -
16A GLU* 2.8 40.9 + - - +
47A THR* 3.0 30.1 + - - +
48A GLU* 3.9 8.3 - - - +
50A ALA* 1.3 74.5 - - - +
52A THR* 1.3 57.8 + - - +
54A VAL* 3.4 8.2 + - - +
55A ALA* 2.9 29.3 + - - +
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Residues in contact with THR 52 (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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48A GLU 3.1 12.9 + - - -
49A PHE* 3.6 18.3 - - + -
50A ALA 3.2 0.2 - - - -
51A LYS* 1.3 78.9 - - - +
53A CYS* 1.3 57.0 + - - +
55A ALA* 3.2 7.1 + - - +
56A ASP* 2.8 28.4 + - + +
59A ALA* 3.9 23.1 - - + -
62A CYS* 5.0 2.2 - - - -
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Residues in contact with CYS 53 (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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5A SER* 3.8 15.9 - - - +
7A VAL* 3.7 13.5 - - + -
8A ALA* 4.0 4.9 - - + -
49A PHE* 3.2 30.1 + - - +
50A ALA 3.1 7.6 + - - +
52A THR* 1.3 76.1 - - - +
54A VAL* 1.3 64.8 + - - +
56A ASP 3.6 2.0 - - - -
57A GLU* 3.0 30.8 + - - +
62A CYS* 2.0 53.6 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.9 16.8 - - - -
11A PHE* 3.7 30.1 - - + -
12A LYS* 3.9 32.1 + - + +
50A ALA 2.9 18.2 + - - +
51A LYS* 3.7 8.5 - - - +
53A CYS* 1.3 78.0 - - - +
55A ALA* 1.3 63.0 + - - +
56A ASP* 3.4 0.3 + - - -
57A GLU* 4.2 10.0 + - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS 2.9 16.9 + - - +
52A THR* 3.6 6.7 - - - +
54A VAL* 1.3 77.5 - - - +
56A ASP* 1.3 63.9 + - + +
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Residues in contact with ASP 56 (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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52A THR* 2.8 15.6 + - + +
53A CYS* 3.1 8.0 - - - +
54A VAL 3.3 0.2 - - - -
55A ALA* 1.3 78.8 - - + +
57A GLU* 1.3 59.0 + - - +
58A SER* 2.7 29.7 + - - -
59A ALA* 3.0 37.7 + - + +
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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