Contacts of the helix formed by residues 33 - 50 (chain D) in PDB entry 5IYB
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 LEU 33 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 1.3 76.7 - - - +
34D ASN* 1.3 66.3 + - - +
35D SER* 3.2 20.6 - - - +
36D GLU* 2.9 59.5 + - + +
37D VAL* 3.1 14.8 + - - +
74D PHE* 4.9 11.9 - - + -
80D ILE* 3.9 15.9 - - + +
83D VAL* 5.9 2.5 - - + -
84D ARG* 3.4 29.8 - - + +
97D LEU* 6.1 0.2 - - + -
98D ALA* 5.6 1.1 - - - +
101D ALA* 4.6 25.1 - - + +
102D ASN* 4.5 8.7 - - - +
2G PHE* 4.6 1.1 - - - -
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 1.3 73.3 - - - +
35D SER* 1.3 57.3 + - - +
37D VAL* 4.7 0.4 - - - -
38D HIS* 3.1 19.1 + - - +
67D TYR* 4.3 9.7 + - - -
68D THR* 2.8 32.8 + - - +
71D PHE* 3.7 44.8 + - - +
72D SER* 4.9 0.9 - - - -
73D ARG* 5.1 5.1 - - + +
102D ASN* 3.3 27.4 + - - +
2G PHE* 3.0 29.3 - - - -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.2 16.1 - - - +
34D ASN* 1.3 76.2 - - - +
36D GLU* 1.3 60.8 + - - +
38D HIS* 3.7 3.3 + - - +
39D MET* 3.1 27.4 + - - +
72D SER* 3.8 8.2 + - - -
73D ARG* 3.3 11.4 + - - +
74D PHE* 3.1 35.2 + - - +
80D ILE* 3.6 24.3 - - - +
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.3 28.8 - - + +
33D LEU* 2.9 31.8 + - + +
35D SER* 1.3 70.8 - - - +
37D VAL* 1.3 66.9 + - - +
39D MET* 3.4 15.9 + - + +
40D LEU* 3.0 33.2 + - + +
80D ILE* 3.4 26.5 - - + +
84D ARG* 3.5 32.7 + - - +
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.9 19.5 - - + -
33D LEU 3.1 10.5 + - - +
36D GLU* 1.3 74.1 - - - +
38D HIS* 1.3 54.5 + - - +
40D LEU* 3.1 9.2 + - - +
41D LEU* 2.8 63.8 + - + +
64D THR* 5.2 0.7 - - + -
68D THR* 4.1 13.7 - - - +
2G PHE* 3.5 47.6 - - + -
46G ILE* 5.1 2.5 - - + -
75G ILE* 4.6 12.1 - - + -
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Residues in contact with HIS 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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34D ASN 3.1 21.1 + - - +
35D SER* 3.7 6.1 + - - +
36D GLU 3.3 0.2 - - - -
37D VAL* 1.3 77.7 - - - +
39D MET* 1.3 53.6 + - - +
41D LEU* 3.4 2.4 + - - +
42D GLU* 2.8 53.8 + - - +
65D LEU* 3.9 13.3 - - + +
68D THR* 3.5 22.4 + - + +
69D ALA* 3.6 34.3 - - + +
72D SER* 3.9 15.9 + - - +
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Residues in contact with MET 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 3.1 18.9 + - - +
36D GLU* 3.5 20.6 - - + +
38D HIS* 1.3 77.6 + - - +
40D LEU* 1.3 73.7 + - + +
42D GLU* 3.3 14.4 + - - +
43D HIS* 2.9 29.0 + - + +
77D ARG* 3.7 55.9 - - + +
80D ILE* 5.6 5.4 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 4.7 13.5 - - + -
36D GLU* 3.0 27.6 + - + +
37D VAL* 3.5 7.6 - - - +
39D MET* 1.3 89.6 - - + +
41D LEU* 1.3 52.2 + - - +
43D HIS* 3.1 12.1 + - + +
44D ARG* 2.7 35.4 + - - +
4G HIS* 5.5 2.9 - - + -
49G THR* 5.0 11.4 - - + -
75G ILE* 3.6 33.7 - - + -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 2.8 40.1 + - + +
38D HIS 3.9 2.7 - - - +
40D LEU* 1.3 70.2 - - - +
42D GLU* 1.3 60.8 + - - +
44D ARG* 3.8 4.0 - - + -
45D LYS* 2.8 29.6 + - - +
61D PHE* 3.4 27.7 - - + +
64D THR* 4.2 9.0 - - + +
65D LEU* 4.0 38.3 - - + +
68D THR* 4.5 2.5 - - + -
46G ILE* 3.7 30.3 - - + -
47G ALA* 4.1 16.4 - - + -
75G ILE* 4.8 5.8 - - + -
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Residues in contact with GLU 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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38D HIS* 2.8 36.1 + - + +
39D MET* 3.5 15.0 - - - +
41D LEU* 1.3 75.6 - - - +
43D HIS* 1.3 59.2 + - - +
45D LYS* 3.5 8.2 + - + +
46D GLN* 2.9 30.8 + - - +
65D LEU* 4.5 6.7 - - + +
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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
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39D MET* 2.9 14.1 + - + +
40D LEU* 3.3 14.4 + - + +
42D GLU* 1.3 75.8 - - - +
44D ARG* 1.3 55.2 + - - +
46D GLN* 3.2 26.4 + - - +
47D GLN* 2.8 66.3 + - + +
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Residues in contact with ARG 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU 2.7 19.6 + - - +
41D LEU* 3.5 13.7 - - + +
43D HIS* 1.3 73.3 + - - +
45D LYS* 1.3 56.9 + - - +
47D GLN* 3.5 11.7 + - - +
48D ASN* 3.0 46.9 + - - +
54D GLU* 6.3 0.4 - - - +
57D LEU* 3.4 23.3 - - + +
61D PHE* 3.7 20.2 - - + -
31G PHE* 3.9 30.7 - - - +
35G GLU* 3.0 35.4 + - - +
47G ALA* 4.6 11.7 - - + -
48G VAL 5.1 7.6 - - - -
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Residues in contact with LYS 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 LEU 2.8 17.9 + - - +
42D GLU* 3.6 9.0 - - + +
43D HIS 3.2 0.2 - - - -
44D ARG* 1.3 72.9 - - - +
46D GLN* 1.3 56.7 + - - +
48D ASN* 3.1 8.3 + - + +
49D GLU* 2.8 66.7 + - + +
56D GLU* 4.1 17.2 + - - +
57D LEU* 4.8 1.8 - - + -
61D PHE* 4.1 16.1 - - + -
62D MET* 4.6 14.4 - - - +
65D LEU* 4.1 22.2 - - + -
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Residues in contact with GLN 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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42D GLU* 2.9 22.3 + - - +
43D HIS* 3.4 27.8 + - - +
45D LYS* 1.3 76.1 - - - +
47D GLN* 1.3 57.8 + - - +
49D GLU* 3.7 12.6 - - - +
50D SER* 2.7 41.5 + - - +
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Residues in contact with GLN 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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43D HIS* 2.8 53.9 + - + +
44D ARG* 3.7 16.2 - - - +
45D LYS 3.2 0.2 - - - -
46D GLN* 1.3 78.8 - - - +
48D ASN* 1.3 63.8 + - - +
50D SER* 3.4 12.2 + - - -
51D ALA* 3.1 24.8 + - - +
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Residues in contact with ASN 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 ARG* 3.0 38.7 + - - +
45D LYS* 3.1 11.9 + - + +
47D GLN* 1.3 74.6 - - - +
49D GLU* 1.3 68.0 + - + +
51D ALA* 3.3 16.3 - - - +
52D GLU 3.7 2.8 + - - -
54D GLU* 3.9 20.3 + - - +
55D GLN 3.5 25.8 + - - +
56D GLU* 3.8 25.2 + - - +
57D LEU* 3.9 15.6 - - + +
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Residues in contact with GLU 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 LYS* 2.8 55.8 + - + +
46D GLN* 3.7 11.2 - - + +
48D ASN* 1.3 69.9 - - + +
50D SER* 1.3 60.2 + - - +
51D ALA 2.8 10.5 + - - -
52D GLU* 3.1 20.6 + - - +
56D GLU* 6.0 2.2 - - - +
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Residues in contact with SER 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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46D GLN* 2.7 27.6 + - - +
47D GLN* 3.4 19.1 + - - -
49D GLU* 1.3 71.3 - - - +
51D ALA* 1.3 59.0 + - - +
52D GLU* 3.5 13.4 - - - +
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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