Contacts of the helix formed by residues 24 - 44 (chain A) in PDB entry 2X5N
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 THR 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A MET 3.9 4.9 - - - -
17A ILE* 3.6 22.4 - - + +
18A ASN 3.2 9.2 - - - +
19A GLY* 4.8 0.9 - - - -
21A TYR 3.1 9.6 - - - -
23A PRO* 1.3 86.4 - - + +
25A ARG* 1.3 64.9 + - - +
26A PHE* 3.4 5.2 + - - +
27A GLU* 3.0 29.3 + - + +
28A ALA* 2.9 24.6 + - - +
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Residues in contact with ARG 25 (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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15A TRP* 3.4 23.0 + - - +
16A MET* 3.4 29.4 + - + +
18A ASN* 2.9 27.9 + - - +
20A ASP* 2.8 44.6 + - - +
21A TYR* 3.5 19.8 + - + -
24A THR* 1.3 70.7 - - - +
26A PHE* 1.3 64.0 + - - +
28A ALA* 3.7 1.4 - - - +
29A GLN* 3.0 24.3 + - - +
115A GLY 2.9 23.6 + - - -
144A ILE* 4.0 13.3 - - + +
145A GLY* 3.3 19.8 - - - -
146A GLU* 2.9 35.8 + - - -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.1 18.4 - - + -
11A ASP 3.5 8.5 - - - -
12A ASN* 3.9 14.6 - - + -
16A MET* 3.0 24.6 + - + +
17A ILE* 5.5 0.4 - - - -
24A THR* 3.2 4.9 - - - +
25A ARG* 1.3 77.2 - - - +
27A GLU* 1.3 79.4 + - + +
29A GLN* 3.3 30.7 + - - +
30A LYS* 3.0 36.9 + - + +
76A MET* 5.1 9.0 - - + -
79A LEU* 4.3 11.7 - - + -
81A VAL* 3.8 38.6 - - + -
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Residues in contact with GLU 27 (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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23A PRO* 3.7 27.9 - - + +
24A THR* 3.0 22.6 + - + +
26A PHE* 1.3 92.9 - - + +
28A ALA* 1.3 63.9 + - - +
30A LYS* 3.3 26.1 + - - +
31A ASP* 3.2 30.0 + - - +
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Residues in contact with ALA 28 (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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21A TYR* 4.0 13.0 - - + -
22A ILE 3.6 19.1 - - - +
23A PRO* 4.3 1.6 - - - +
24A THR 2.9 18.0 + - - +
25A ARG 3.7 3.6 - - - +
27A GLU* 1.3 74.9 - - - +
29A GLN* 1.3 63.7 + - - +
31A ASP* 3.6 6.2 + - - +
32A THR* 2.9 26.0 + - - -
178A LEU* 3.9 27.5 - - + +
179A SER 4.5 1.2 + - - -
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.5 16.5 - - + +
11A ASP 2.8 45.2 + - - +
16A MET* 3.7 11.4 - - + +
25A ARG 3.0 11.2 + - - +
26A PHE* 3.3 30.5 + - - +
28A ALA* 1.3 78.4 - - - +
30A LYS* 1.3 63.8 + - - +
32A THR* 2.9 5.0 + - - -
33A VAL* 2.9 21.1 + - - +
113A PHE* 3.0 46.7 - - + +
144A ILE* 5.4 0.2 - - + -
178A LEU* 4.0 6.0 - - + +
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Residues in contact with LYS 30 (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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10A ILE* 5.9 0.7 - - - -
26A PHE* 3.0 27.0 + - + +
27A GLU* 3.3 36.5 + - - +
29A GLN* 1.3 78.3 - - - +
31A ASP* 1.3 64.6 + - - +
33A VAL* 3.4 20.9 + - - +
34A HIS* 3.6 4.3 + - - +
69A TYR* 3.8 5.8 + - - +
73A LEU* 4.2 18.3 + - + +
76A MET* 4.0 47.2 + - + +
77A HIS* 5.9 1.6 - - - +
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Residues in contact with ASP 31 (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 GLU* 3.2 14.9 + - - +
28A ALA* 3.9 8.5 - - - +
29A GLN 3.2 0.2 - - - -
30A LYS* 1.3 80.7 - - - +
32A THR* 1.3 61.3 + - - +
34A HIS* 3.3 15.9 + - - +
35A MET* 3.5 8.8 + - - +
177A LEU* 5.8 3.5 - - - +
179A SER* 4.0 20.3 + - - +
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Residues in contact with THR 32 (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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28A ALA 2.9 14.3 + - - -
29A GLN 2.9 9.5 + - - -
31A ASP* 1.3 75.6 - - - +
33A VAL* 1.3 65.8 + - - +
35A MET* 3.1 14.0 + - + +
36A ILE* 3.0 20.8 + - + +
113A PHE* 3.7 24.7 - - + -
142A ILE* 4.3 2.2 - - + -
178A LEU* 3.7 6.2 - - - +
179A SER* 3.2 24.3 + - - -
182A VAL* 3.9 32.3 - - + -
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Residues in contact with VAL 33 (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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8A ILE* 4.2 15.4 - - + +
10A ILE* 3.5 30.5 - - + -
29A GLN 2.9 19.0 + - - +
30A LYS* 3.5 12.3 - - - +
31A ASP 3.3 0.4 - - - -
32A THR* 1.3 76.3 - - - +
34A HIS* 1.3 56.6 + - - +
36A ILE* 3.3 6.6 + - - +
37A PHE* 2.9 28.1 + - - +
51A LEU* 4.5 4.7 - - + -
69A TYR* 3.5 12.8 - - + +
72A PHE* 3.9 25.1 - - + -
76A MET* 4.9 5.2 - - + -
113A PHE* 3.7 16.2 - - + -
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Residues in contact with HIS 34 (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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30A LYS 3.6 3.0 + - - +
31A ASP* 3.3 12.0 + - - +
32A THR 3.2 0.8 - - - -
33A VAL* 1.3 78.5 - - - +
35A MET* 1.3 57.4 + - - +
37A PHE* 3.5 0.5 + - - +
38A ASN* 3.0 55.5 + - - -
69A TYR* 3.4 54.7 + + - +
73A LEU* 5.4 3.1 - - + +
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Residues in contact with MET 35 (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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31A ASP 3.5 7.8 + - - +
32A THR* 3.1 17.4 + - + +
34A HIS* 1.3 80.4 - - - +
36A ILE* 1.3 84.3 + - + +
38A ASN* 3.4 5.7 + - - +
39A GLN* 2.9 24.9 + - - +
179A SER* 4.2 7.9 - - - +
182A VAL* 3.6 24.0 - - + +
183A ASN* 3.6 35.4 - - + +
187A ILE 4.5 0.4 - - - +
188A GLY* 4.1 9.4 - - - -
189A GLN* 3.4 31.3 - - - +
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Residues in contact with ILE 36 (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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8A ILE* 3.8 20.6 - - + -
32A THR* 3.0 20.0 + - + +
33A VAL* 3.7 8.3 - - - +
35A MET* 1.3 95.4 - - + +
37A PHE* 1.3 64.6 + - - +
39A GLN* 3.1 7.5 + - + +
40A LYS* 3.0 32.8 + - + +
111A VAL* 4.2 30.5 - - + -
113A PHE* 5.1 2.0 - - + -
142A ILE* 4.7 2.9 - - + -
182A VAL* 4.5 1.6 - - + -
187A ILE* 3.9 39.5 - - + +
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Residues in contact with PHE 37 (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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8A ILE* 4.1 4.2 - - + +
33A VAL 2.9 17.9 + - - +
34A HIS 3.6 4.0 - - - +
36A ILE* 1.3 75.9 - - - +
38A ASN* 1.3 71.2 + - - +
40A LYS* 3.2 3.3 + - - +
41A ILE* 2.9 42.9 + - + +
49A CYS* 3.6 30.7 - - + -
66A THR* 3.9 6.3 - - + -
67A ARG* 3.5 36.8 - - - -
68A ASP 3.9 0.4 - - - -
69A TYR* 3.5 42.4 - + + -
72A PHE* 3.7 33.0 - + - -
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Residues in contact with ASN 38 (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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34A HIS* 3.0 47.1 + - - +
35A MET* 3.8 5.5 - - - +
37A PHE* 1.3 83.5 - - - +
39A GLN* 1.3 65.9 + - - +
41A ILE* 4.4 7.1 - - - +
42A ASN* 2.9 39.8 + - - +
69A TYR* 5.4 0.3 - - - +
189A GLN* 3.9 16.1 - - - +
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Residues in contact with GLN 39 (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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4A GLU* 5.2 0.4 + - - -
35A MET* 2.9 14.8 + - - +
36A ILE* 3.1 12.9 + - - +
38A ASN* 1.3 76.0 - - - +
40A LYS* 1.3 98.2 + - - +
42A ASN* 3.8 4.1 - - - +
43A ASP* 3.1 43.0 + - - +
187A ILE 4.3 11.2 - - - +
188A GLY 3.8 22.7 - - - +
189A GLN* 4.0 23.4 - - + +
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Residues in contact with LYS 40 (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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4A GLU* 2.8 30.0 + - + +
6A THR* 3.4 27.6 - - + +
36A ILE* 3.0 21.3 + - + +
37A PHE 3.6 1.3 - - - +
39A GLN* 1.3 103.2 + - - +
41A ILE* 1.3 62.9 + - + +
43A ASP* 3.1 7.2 + - + -
44A ASN 3.8 0.2 + - - -
47A ASN* 3.0 34.5 + - + +
48A MET 5.3 0.4 - - - +
49A CYS* 3.5 31.4 - - - -
109A ARG* 3.5 21.2 - - - +
111A VAL* 4.8 2.0 - - - -
140A ASP* 5.0 2.0 + - - -
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Residues in contact with ILE 41 (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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37A PHE* 2.9 51.5 + - + +
38A ASN* 4.1 8.1 - - - +
40A LYS* 1.3 78.7 - - + +
42A ASN* 1.3 75.3 + - - +
44A ASN 3.3 9.0 + - - +
47A ASN 4.0 13.9 - - - +
49A CYS* 4.1 14.1 - - - -
66A THR 4.3 1.8 - - - +
67A ARG* 2.9 62.6 + - + +
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Residues in contact with ASN 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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38A ASN* 2.9 33.5 + - - +
39A GLN* 3.8 4.3 - - - +
41A ILE* 1.3 89.1 - - - +
43A ASP* 1.3 59.8 + - - +
44A ASN 3.4 0.7 - - - -
189A GLN* 4.4 8.7 - - - +
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Residues in contact with ASP 43 (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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2A VAL* 2.9 39.5 + - - +
4A GLU* 5.1 1.4 - - - +
39A GLN* 3.1 32.5 + - - +
40A LYS* 3.1 9.0 + - + +
42A ASN* 1.3 80.2 - - - +
44A ASN* 1.3 61.5 + - - +
47A ASN* 3.7 9.1 + - - +
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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
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2A VAL 3.6 7.9 - - - +
3A LEU* 3.6 30.3 - - - +
40A LYS 3.8 1.2 + - - -
41A ILE 3.3 5.7 - - - +
42A ASN 3.4 1.0 - - - -
43A ASP* 1.3 81.8 + - - +
45A PRO* 1.3 73.3 - - - +
46A GLU* 2.9 35.3 + - - +
47A ASN* 3.1 22.4 + - - +
67A ARG* 3.0 19.4 + - - -
1194A SO4 5.1 3.2 + - - -
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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