Contacts of the helix formed by residues 27 - 50 (chain A) in PDB entry 5B82
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 ASN 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 1.3 74.9 - - - +
28A PRO* 1.3 75.8 - - + +
29A GLU* 3.2 11.9 + - - +
30A GLU* 2.7 45.0 + - - +
31A LEU* 3.0 26.6 + - - +
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Residues in contact with PRO 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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27A ASN* 1.3 88.4 - - + +
29A GLU* 1.3 64.3 + - - +
31A LEU* 3.2 14.4 + - + +
32A GLY* 3.0 19.9 + - - -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 3.2 8.8 + - - +
28A PRO* 1.3 80.4 - - - +
30A GLU* 1.3 58.5 + - - +
32A GLY* 3.4 1.5 + - - -
33A LYS* 2.9 33.1 + - + +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.3 21.5 + - - -
27A ASN* 2.7 33.7 + - - +
29A GLU* 1.3 71.2 - - - +
31A LEU* 1.3 64.8 + - - +
33A LYS* 3.3 8.0 + - + +
34A VAL* 2.9 23.2 + - - +
82A ASN 4.5 3.8 - - - +
84A TRP* 2.9 33.1 + - + +
180A ILE* 3.7 26.7 - - + +
184A GLN* 5.3 2.4 + - - -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.3 9.9 - - + -
27A ASN* 3.0 21.1 + - - +
28A PRO* 3.2 11.0 + - + +
30A GLU* 1.3 75.0 - - - +
32A GLY* 1.3 64.8 + - - +
34A VAL* 3.1 9.5 + - + +
35A VAL* 3.0 25.7 + - - +
122A TRP* 3.9 37.9 - - + +
129A VAL* 4.0 27.4 - - + -
180A ILE* 4.0 13.7 - - + -
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Residues in contact with GLY 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 PRO 3.0 13.4 + - - -
29A GLU* 3.8 3.1 - - - -
31A LEU* 1.3 79.0 - - - +
33A LYS* 1.3 54.7 + - - +
35A VAL* 3.2 9.0 + - - +
36A THR* 2.9 34.0 + - - -
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Residues in contact with LYS 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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29A GLU* 2.9 23.2 + - + +
30A GLU* 3.5 9.6 - - + +
31A LEU 3.3 0.2 - - - -
32A GLY* 1.3 75.5 - - - +
34A VAL* 1.3 58.0 + - - +
36A THR* 3.9 5.6 - - - -
37A ALA* 2.9 32.0 + - + +
82A ASN* 3.2 31.8 + - - +
84A TRP* 3.6 12.6 - - + -
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Residues in contact with VAL 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 GLU 2.9 19.5 + - - +
31A LEU* 3.1 8.3 + - + +
33A LYS* 1.3 75.5 - - - +
35A VAL* 1.3 65.0 + - + +
37A ALA* 3.3 1.4 + - - +
38A ILE* 3.0 23.6 + - - +
84A TRP* 3.5 38.1 - - + -
131A TYR* 3.7 31.6 - - + -
178A VAL* 3.9 22.2 - - + -
180A ILE* 4.0 19.7 - - + -
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Residues in contact with VAL 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 LEU 3.0 15.7 + - - +
32A GLY* 3.2 8.9 + - - +
34A VAL* 1.3 76.1 - - + +
36A THR* 1.3 60.2 + - - +
38A ILE* 3.4 1.7 + - - +
39A GLU* 2.9 35.0 + - + +
122A TRP* 5.6 5.8 - - + +
131A TYR* 3.8 43.3 + - + +
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Residues in contact with THR 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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32A GLY 2.9 17.8 + - - -
33A LYS* 3.9 5.8 - - - -
35A VAL* 1.3 77.7 - - - +
37A ALA* 1.3 58.4 + - - +
39A GLU* 3.3 5.4 + - + +
40A GLN* 2.9 54.2 + - + +
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Residues in contact with ALA 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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33A LYS* 2.9 22.1 + - + +
34A VAL 3.7 2.9 - - - +
36A THR* 1.3 75.1 - - - +
38A ILE* 1.3 61.7 + - + +
40A GLN* 3.3 13.4 + - - +
41A LEU* 3.0 27.7 + - - +
78A ILE* 4.4 23.9 - - + +
84A TRP* 4.3 18.2 - - + -
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Residues in contact with ILE 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 VAL* 3.0 19.9 + - + +
35A VAL 3.9 2.9 - - - +
37A ALA* 1.3 80.9 - - + +
39A GLU* 1.3 62.6 + - - +
41A LEU* 3.1 15.2 + - + +
42A ASP* 2.9 21.1 + - - +
78A ILE* 5.7 4.3 - - + -
84A TRP* 6.4 0.4 - - + -
86A VAL* 4.2 16.2 - - + -
131A TYR* 4.0 13.0 - - + -
133A ARG* 3.9 19.7 - - + -
176A TYR* 3.5 41.0 - - + -
178A VAL* 3.5 33.9 - - + -
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Residues in contact with GLU 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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35A VAL* 2.9 23.9 + - + +
36A THR* 3.8 5.2 - - - +
38A ILE* 1.3 77.4 - - - +
40A GLN* 1.3 56.7 + - - +
42A ASP* 3.3 8.9 + - - +
43A GLN* 2.9 47.3 + - + +
131A TYR* 4.6 4.3 + - - -
133A ARG* 2.8 50.3 + - - +
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Residues in contact with GLN 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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36A THR* 2.9 39.2 + - + +
37A ALA* 3.6 12.3 - - - +
39A GLU* 1.3 73.4 - - - +
41A LEU* 1.3 60.8 - - - +
43A GLN* 3.5 5.8 + - - +
44A MET* 2.9 28.8 + - - +
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Residues in contact with LEU 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 ALA 3.0 13.4 + - - +
38A ILE* 3.4 19.1 - - + +
40A GLN* 1.3 77.6 - - - +
42A ASP* 1.3 56.8 + - - +
44A MET* 3.2 12.5 + - - +
45A ARG* 3.0 26.7 + - - +
71A VAL* 3.6 46.4 - - + +
74A GLN* 3.7 26.0 - - + -
75A ALA* 4.2 17.7 - - + -
78A ILE* 4.9 7.2 - - + -
86A VAL* 5.0 2.0 - - + -
88A GLN* 5.6 0.9 - - + -
176A TYR* 3.9 25.8 - - + -
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Residues in contact with ASP 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 ILE 2.9 12.4 + - - +
39A GLU* 3.5 14.6 - - - +
41A LEU* 1.3 74.9 - - - +
43A GLN* 1.3 62.3 + - + +
45A ARG* 3.2 6.5 + - - +
46A ILE* 3.0 48.2 + - - +
133A ARG* 4.3 21.7 + - - +
134A ARG 5.2 1.7 - - - +
135A ILE* 4.4 12.1 - - - +
176A TYR* 2.6 40.1 + - + +
501A HEC 6.0 0.2 - - - +
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Residues in contact with GLN 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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39A GLU* 2.9 33.3 + - + +
40A GLN* 4.0 5.8 - - - +
42A ASP* 1.3 79.2 + - + +
44A MET* 1.3 57.3 + - - +
46A ILE* 3.8 26.3 - - - +
47A GLY* 2.9 25.8 + - - -
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Residues in contact with MET 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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40A GLN 2.9 15.6 + - - +
41A LEU* 3.3 20.4 - - - +
42A ASP 3.1 0.2 - - - -
43A GLN* 1.3 74.9 - - - +
45A ARG* 1.3 67.4 + - - +
47A GLY* 3.2 2.6 + - - -
48A LEU* 2.9 38.6 + - + +
70A PRO* 3.5 47.3 - - + +
71A VAL* 3.8 5.8 - - + +
74A GLN* 3.7 23.1 - - + +
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Residues in contact with ARG 45 (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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41A LEU 3.0 10.6 + - - +
42A ASP* 3.2 8.9 + - - +
44A MET* 1.3 76.0 - - - +
46A ILE* 1.3 64.7 + - + +
48A LEU* 3.0 6.8 + - - +
49A ALA* 2.9 22.2 + - - +
67A VAL* 4.1 7.8 - - + +
68A CYS* 3.3 33.7 - - - +
71A VAL* 3.7 28.2 - - + +
88A GLN* 2.8 30.1 + - - -
135A ILE* 3.8 3.0 - - - +
176A TYR* 3.0 33.7 + - - -
501A HEC 3.4 62.8 - - - +
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Residues in contact with ILE 46 (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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42A ASP* 3.0 39.3 + - - +
43A GLN* 3.8 27.8 - - - +
45A ARG* 1.3 76.5 - - + +
47A GLY* 1.3 58.3 + - - +
49A ALA* 3.4 1.6 + - - +
50A SER* 2.9 31.4 + - - -
138A GLN* 3.8 32.1 - - + +
140A SER* 5.2 0.9 + - - -
501A HEC 4.4 10.8 - - + -
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Residues in contact with GLY 47 (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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43A GLN 2.9 15.6 + - - -
44A MET* 3.5 3.8 - - - -
45A ARG 3.1 0.2 - - - -
46A ILE* 1.3 77.7 - - - +
48A LEU* 1.3 62.0 + - - +
50A SER* 2.9 24.3 + - - -
51A THR* 4.6 1.4 + - - +
65A LYS* 4.7 2.1 + - - -
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Residues in contact with LEU 48 (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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44A MET* 2.9 37.9 + - + +
45A ARG 3.7 5.8 - - - +
47A GLY* 1.3 75.3 - - - +
49A ALA* 1.3 62.1 + - - +
50A SER 3.4 0.5 + - - -
51A THR* 3.7 0.5 + - - -
52A LEU* 4.8 0.2 - - - +
65A LYS* 2.5 44.8 + - - +
66A ALA 4.1 8.1 - - - +
67A VAL* 3.5 35.1 - - + +
70A PRO* 3.8 19.1 - - + -
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Residues in contact with ALA 49 (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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45A ARG 2.9 15.0 + - - +
46A ILE 3.7 2.0 - - - +
48A LEU* 1.3 77.1 - - - +
50A SER* 1.3 64.2 + - - +
51A THR 3.2 0.2 - - - -
52A LEU* 3.0 20.2 + - - +
67A VAL* 4.0 19.7 - - + +
140A SER* 3.3 30.5 - - - +
501A HEC 3.8 26.2 - - + -
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Residues in contact with SER 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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46A ILE* 2.9 20.5 + - - -
47A GLY* 2.9 19.0 + - - -
48A LEU 3.2 0.6 - - - -
49A ALA* 1.3 76.1 - - - +
51A THR* 1.3 66.3 + - - +
52A LEU 3.1 7.1 + - - +
140A SER* 4.7 4.9 - - - -
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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