Contacts of the helix formed by residues 35 - 55 (chain G) in PDB entry 4B2Q
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 GLU 35 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.1 34.9 - - + +
32G SER* 3.1 16.6 + - - +
34G ALA* 1.3 77.2 - - - +
36G LYS* 1.3 63.6 + - + +
37G ALA 3.2 0.2 - - - -
38G LYS* 4.0 15.6 + - - +
39G ILE* 2.8 47.5 + - + +
227G ALA* 4.0 13.9 - - - +
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Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G SER 3.7 11.2 + - - +
33G LYS* 4.2 12.3 + - + +
34G ALA 3.4 0.2 - - - -
35G GLU* 1.3 80.7 - - + +
37G ALA* 1.3 57.9 + - - +
39G ILE* 5.1 3.1 - - + -
40G SER* 3.1 32.8 + - - -
18H HIS* 4.7 2.1 - - - +
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Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LYS 4.2 4.4 + - - +
34G ALA* 3.6 11.5 + - - +
35G GLU 3.2 0.4 - - - -
36G LYS* 1.3 78.6 - - - +
38G LYS* 1.3 57.0 + - - +
40G SER* 4.4 4.3 - - - -
41G ALA* 3.4 13.6 + - - +
137G ALA* 4.2 25.6 - - + -
138G PRO 5.0 5.6 - - - +
223G ALA* 3.3 28.5 - - + +
17H PRO 5.3 1.7 - - - +
18H HIS* 6.4 0.9 - - - +
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Residues in contact with LYS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ALA 3.0 16.5 + - - +
35G GLU* 3.2 21.0 + - - +
37G ALA* 1.3 80.1 - - - +
39G ILE* 1.3 73.8 + - + +
41G ALA* 3.4 4.2 + - - +
42G LYS* 3.1 40.1 + - - +
168G ASP* 5.9 0.2 + - - -
169G PRO* 3.6 31.6 + - - -
220G THR* 5.7 0.3 - - - +
223G ALA 4.0 10.3 - - - +
224G GLN* 3.8 28.9 + - + +
227G ALA* 3.8 17.9 - - + -
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Residues in contact with ILE 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G GLU* 2.8 34.1 + - + +
36G LYS* 4.8 3.4 - - + +
38G LYS* 1.3 84.5 - - + +
40G SER* 1.3 60.2 + - - +
41G ALA 3.1 0.2 - - - -
42G LYS* 3.9 23.0 - - - +
43G LYS* 3.0 58.5 + - + +
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Residues in contact with SER 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LYS 3.1 21.5 + - - -
37G ALA* 4.9 2.0 - - - -
38G LYS 3.4 0.2 - - - -
39G ILE* 1.3 78.1 - - - +
41G ALA* 1.3 57.3 + - - +
44G MET* 3.4 15.8 + - - +
16H LEU 3.1 17.9 - - - +
17H PRO* 4.2 4.7 - - - +
18H HIS* 3.3 35.9 + - - -
19H GLU* 3.9 10.3 + - - -
20H THR* 4.3 12.3 + - - +
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Residues in contact with ALA 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ALA 3.4 20.3 + - - +
38G LYS* 3.4 5.2 + - - +
39G ILE 3.1 0.6 - - - -
40G SER* 1.3 80.8 - - - +
42G LYS* 1.3 58.7 + - - +
44G MET* 4.2 6.8 - - + +
45G ASP* 3.1 16.6 + - - +
219G LEU* 4.5 10.5 - - + +
220G THR* 2.9 39.1 + - + +
223G ALA* 4.2 14.1 - - + -
224G GLN* 6.3 0.4 - - + -
17H PRO* 5.3 4.0 - - - +
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Residues in contact with LYS 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G LYS* 3.1 30.3 + - + +
39G ILE* 3.9 23.3 - - - +
41G ALA* 1.3 76.3 - - - +
43G LYS* 1.3 81.2 + - - +
44G MET 3.2 0.2 - - - -
45G ASP* 3.0 8.9 + - + +
46G GLU* 2.8 51.5 + - + +
220G THR* 4.4 6.5 - - + +
224G GLN* 5.1 9.6 - - - +
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Residues in contact with LYS 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ILE* 3.0 39.9 + - + +
42G LYS* 1.3 91.5 - - - +
44G MET* 1.3 62.0 + - - +
46G GLU* 3.4 21.4 + - - +
47G ALA* 3.4 17.2 + - - +
15H ALA* 4.7 3.9 - - + +
20H THR* 3.7 25.5 + - + +
23H SER* 5.5 7.9 - - - +
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Residues in contact with MET 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G SER 3.4 18.9 + - - +
41G ALA* 4.2 7.9 - - - +
42G LYS 3.2 0.4 - - - -
43G LYS* 1.3 76.2 - - - +
45G ASP* 1.3 68.2 + - - +
47G ALA* 3.1 18.7 + - + +
48G GLU* 3.5 6.2 + - - +
216G ASN* 3.0 38.6 - - + +
219G LEU* 4.7 9.0 - - + -
220G THR* 4.9 4.7 - - - +
15H ALA* 4.0 22.1 - - + +
16H LEU* 3.6 8.5 - - - +
17H PRO* 3.3 44.0 - - + -
86H THR* 4.3 15.5 + - + +
87H ALA 4.2 5.8 - - - +
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Residues in contact with ASP 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ALA 3.1 21.5 + - - +
42G LYS* 3.0 12.1 + - - +
44G MET* 1.3 80.7 - - - +
46G GLU* 1.3 60.6 + - - +
48G GLU* 3.2 5.3 + - - +
49G GLN* 2.9 44.0 + - - +
180G LYS* 5.2 1.8 + - - -
216G ASN* 5.7 1.5 - - - +
217G GLN* 2.8 41.7 + - - +
220G THR* 3.6 21.0 + - + +
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G LYS* 2.8 35.4 + - + +
43G LYS* 3.6 29.4 - - - +
44G MET 3.3 0.4 - - - -
45G ASP* 1.3 79.4 - - + +
47G ALA* 1.3 57.4 + - - +
49G GLN* 4.4 6.1 - - - -
50G LEU* 3.0 30.7 + - - +
13H GLN* 4.9 4.3 - - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LYS 3.4 7.7 + - - +
44G MET* 3.1 18.0 + - + +
46G GLU* 1.3 81.3 - - - +
48G GLU* 1.3 61.1 + - - +
50G LEU* 3.7 10.9 - - - +
51G PHE* 4.3 3.6 + - - +
13H GLN* 4.4 31.9 - - + +
15H ALA* 5.2 4.0 - - + -
76H THR* 6.1 0.3 - - - -
84H CYS* 3.8 20.0 - - + +
85H VAL 5.0 0.9 - - - +
86H THR* 3.8 15.7 - - - +
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Residues in contact with GLU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G MET 3.5 5.3 + - - +
45G ASP* 3.2 8.0 + - - +
47G ALA* 1.3 77.9 - - - +
49G GLN* 1.3 64.7 + - - +
50G LEU 3.3 0.2 - - - -
51G PHE* 3.5 11.1 + - - +
52G TYR* 3.2 25.8 - - + -
209G LEU* 4.4 7.1 - - + +
212G TYR* 3.3 29.1 - - + -
213G THR* 3.4 26.4 + - - +
216G ASN* 3.8 19.2 - - + +
217G GLN* 3.1 23.6 + - - +
74H PHE* 4.7 1.9 - - + -
86H THR* 4.3 13.4 + - + +
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Residues in contact with GLN 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ASP* 2.9 37.3 + - - +
46G GLU* 4.3 5.4 - - - +
48G GLU* 1.3 78.3 + - - +
50G LEU* 1.3 65.6 + - - +
51G PHE 3.0 2.7 - - - -
52G TYR* 3.1 38.8 + - - +
53G LYS* 3.2 26.5 + - - +
213G THR* 4.7 2.8 - - - +
217G GLN* 2.9 35.6 - - - +
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Residues in contact with LEU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G GLU 3.0 19.3 + - - +
47G ALA 3.7 6.7 - - - +
48G GLU 3.3 0.2 - - - -
49G GLN* 1.3 76.1 - - - +
51G PHE* 1.3 58.2 + - - +
53G LYS* 3.2 27.2 + - + +
54G ASN* 3.4 12.3 + - - +
13H GLN* 3.5 26.0 - - - +
78H GLN* 2.7 36.1 + - + +
80H ASP* 5.8 0.2 - - - +
82H GLN* 4.3 15.9 - - + +
84H CYS* 3.5 15.7 - - - -
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Residues in contact with PHE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ALA 4.3 2.6 + - - +
48G GLU* 3.5 12.2 + - + +
49G GLN 3.0 0.4 - - - -
50G LEU* 1.3 80.2 - - - +
52G TYR* 1.3 83.0 + + - +
54G ASN* 3.7 1.9 + - - +
55G ALA* 3.1 30.0 + - + +
57G THR* 5.2 10.3 - - + -
188G ILE* 5.5 4.5 - - + -
194G PHE* 5.3 15.3 - + - -
197G PHE* 3.5 26.5 - + + -
209G LEU* 4.2 24.2 - - + -
49H VAL* 3.4 31.6 - - + -
76H THR* 3.5 32.1 - - + +
78H GLN* 3.4 8.5 - - - +
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Residues in contact with TYR 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G GLU* 3.2 33.0 - - + -
49G GLN* 3.1 25.7 + - - +
51G PHE* 1.3 92.3 - + - +
53G LYS* 1.3 63.5 + - + +
55G ALA 2.8 22.4 - - - +
56G GLU* 4.0 3.3 + - - -
57G THR* 3.1 29.5 + - + +
183G PHE* 4.1 29.2 + + + -
188G ILE* 5.7 4.5 - - + +
209G LEU* 4.0 16.1 - - + +
213G THR* 2.8 38.0 + - + +
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G GLN* 3.4 24.0 - - - +
50G LEU* 3.4 21.8 - - + +
51G PHE 3.1 0.8 - - - -
52G TYR* 1.3 78.7 - - + +
54G ASN* 1.3 65.7 + - - +
55G ALA 3.0 7.2 + - - -
56G GLU* 4.1 5.9 + - - +
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Residues in contact with ASN 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G LEU* 3.4 15.4 + - - +
51G PHE 4.4 1.1 - - - +
53G LYS* 1.3 82.4 - - - +
55G ALA* 1.3 57.4 + - - +
56G GLU* 4.0 2.4 + - - +
193G SER* 4.2 8.3 + - - -
196G LYS* 4.2 11.6 - - - -
197G PHE* 4.7 4.3 - - + -
78H GLN* 2.8 44.6 - - - +
79H PRO* 4.2 21.6 - - + +
80H ASP* 3.9 16.3 + - - +
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G PHE* 3.1 23.2 + - + +
52G TYR 2.8 16.7 - - - +
53G LYS 3.0 0.4 - - - -
54G ASN* 1.3 76.7 - - - +
56G GLU* 1.3 69.0 + - - +
57G THR* 3.1 13.7 + - + +
193G SER* 3.2 23.3 - - - +
194G PHE* 6.3 0.7 - - + -
197G PHE* 3.4 24.2 - - + -
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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
------------------------------------------------------------
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