Contacts of the helix formed by residues 38 - 58 (chain E) in PDB entry 4ZZ7
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 SER 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ARG* 5.5 10.4 - - - -
15E GLU* 2.8 35.7 + - - -
17E THR* 4.8 3.1 - - - -
18E ARG* 5.6 0.7 - - - -
36E LEU 3.5 1.7 + - - -
37E ALA* 1.3 76.4 - - - +
39E THR* 1.3 65.9 + - - +
40E LYS* 3.2 13.5 + - - +
41E THR* 3.2 11.3 + - - -
42E VAL* 3.2 12.9 + - - +
206E GLU* 3.2 22.9 - - - -
210E ALA* 5.3 0.2 - - - -
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Residues in contact with THR 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D HIS* 6.3 1.1 - - - +
38E SER* 1.3 75.7 - - - +
40E LYS* 1.3 58.7 + - - +
42E VAL* 3.6 2.3 + - - +
43E GLU* 3.0 42.6 + - - +
206E GLU* 3.2 24.0 + - + +
209E ASP* 6.3 0.4 - - + -
210E ALA* 4.0 28.6 - - + +
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Residues in contact with LYS 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ARG* 5.8 6.5 - - - +
15E GLU* 6.1 0.4 - - - -
38E SER* 3.2 9.0 + - - +
39E THR* 1.3 81.1 + - - +
41E THR* 1.3 64.5 + - - +
43E GLU* 3.3 14.5 + - - +
44E GLN* 3.2 41.6 + - + +
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E HIS* 3.9 29.2 - - + -
8E ILE* 3.8 14.4 - - + +
13E VAL* 5.6 2.0 - - + -
15E GLU* 2.9 36.9 + - + +
37E ALA* 3.9 11.0 - - + -
38E SER* 3.2 9.0 + - - -
40E LYS* 1.3 74.6 - - - +
42E VAL* 1.3 65.4 + - - +
44E GLN* 3.1 22.2 + - - +
45E ALA* 3.2 9.7 + - - +
201E VAL* 3.9 6.5 - - + -
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ALA* 4.2 3.8 - - + -
38E SER 3.2 12.3 + - - +
39E THR 3.7 7.2 - - - +
41E THR* 1.3 76.8 - - - +
43E GLU* 1.3 57.4 + - + +
45E ALA* 3.3 4.5 + - - +
46E ILE* 3.0 42.6 + - + +
170E VAL* 5.3 0.7 - - + -
201E VAL* 4.0 25.1 - - + -
207E ALA* 3.9 28.0 - - + +
210E ALA* 3.7 21.5 - - + -
211E LEU* 4.0 19.1 - - + -
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Residues in contact with GLU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E THR* 3.0 33.3 + - - +
40E LYS* 3.7 13.7 - - - +
41E THR 3.3 0.4 - - - -
42E VAL* 1.3 76.0 - - + +
44E GLN* 1.3 53.3 + - - +
46E ILE* 4.3 3.4 - - + -
47E SER* 2.7 40.0 + - - +
210E ALA* 6.1 1.3 - - + -
214E ASP* 3.6 20.7 - - - +
216E ARG* 3.6 11.5 + - - +
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Residues in contact with GLN 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.8 16.1 - - + +
13E VAL* 5.7 3.8 - - - +
40E LYS* 3.2 37.1 + - + +
41E THR* 3.1 16.3 + - - +
43E GLU* 1.3 76.9 - - + +
45E ALA* 1.3 57.4 + - - +
47E SER* 3.5 7.0 + - - -
48E ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 3.7 31.1 - - + +
41E THR 3.2 6.2 + - - +
42E VAL 3.4 9.6 - - - +
44E GLN* 1.3 76.6 - - - +
46E ILE* 1.3 59.2 + - - +
48E ALA* 3.2 4.3 + - - +
49E ALA* 3.0 24.3 + - - +
170E VAL* 4.0 23.6 - - + -
199E ASN* 3.5 16.2 + - + -
201E VAL* 4.5 7.9 - - + -
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Residues in contact with ILE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E VAL* 3.0 37.8 + - + +
43E GLU* 4.5 0.9 - - + -
45E ALA* 1.3 73.7 - - - +
47E SER* 1.3 57.7 - - - +
49E ALA* 3.2 3.3 + - - +
50E GLN* 2.8 28.2 + - - +
141E VAL* 4.4 9.9 - - + -
170E VAL* 4.3 12.3 - - + -
211E LEU* 4.2 13.0 - - + -
214E ASP* 3.5 30.3 - - + +
216E ARG* 3.4 46.2 - - + +
217E VAL* 3.8 17.9 - - + -
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Residues in contact with SER 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E GLU* 2.7 25.2 + - - +
44E GLN* 3.6 8.5 - - - -
45E ALA 3.3 0.4 - - - -
46E ILE* 1.3 73.3 - - - +
48E ALA* 1.3 56.0 + - - +
50E GLN* 4.0 3.1 - - - +
51E HIS* 3.1 29.8 + - - +
216E ARG* 2.9 25.9 + - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.0 9.0 - - + -
9E ASN* 3.9 33.8 - - + +
44E GLN 2.9 17.9 + - - +
45E ALA 3.4 6.3 - - - +
46E ILE 3.2 0.2 - - - -
47E SER* 1.3 75.0 - - - +
49E ALA* 1.3 58.4 + - - +
51E HIS* 3.5 5.7 + - - +
52E ALA* 3.1 29.5 + - - +
196E GLY* 3.8 5.5 - - - +
199E ASN* 4.0 6.7 - - - +
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Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ALA 3.0 12.8 + - - +
46E ILE 3.5 7.4 - - - +
48E ALA* 1.3 74.0 - - - +
50E GLN* 1.3 65.3 + - - +
52E ALA 3.1 1.9 + - - -
53E PHE* 3.0 24.8 + - - +
141E VAL* 3.8 23.8 - - + -
168E CYS* 3.5 23.3 - - + -
170E VAL* 4.1 5.2 - - + -
196E GLY 3.3 11.1 + - - -
199E ASN* 3.9 9.2 - - - +
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Residues in contact with GLN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE 2.8 19.8 + - - +
47E SER* 4.1 5.8 - - - +
49E ALA* 1.3 73.8 - - - +
51E HIS* 1.3 61.3 + - - +
53E PHE* 3.6 21.2 + - - +
54E PRO* 3.4 20.7 - - - +
140E GLY* 5.5 1.1 - - - -
141E VAL* 3.3 24.4 + - + +
216E ARG* 3.8 36.0 - - - +
218E LYS* 5.7 0.9 - - - +
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Residues in contact with HIS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ASN* 5.9 3.8 - - - -
47E SER 3.1 19.8 + - - +
48E ALA* 3.9 6.3 - - - +
49E ALA 3.1 0.2 - - - -
50E GLN* 1.3 78.7 - - - +
52E ALA* 1.3 60.4 + - + +
53E PHE 3.5 0.5 + - - -
54E PRO* 3.6 10.2 - - - +
55E THR* 5.4 1.4 + - - +
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ASN* 5.4 0.2 - - - +
48E ALA 3.1 18.4 + - - +
49E ALA 3.1 4.2 + - - +
51E HIS* 1.3 78.8 - - + +
53E PHE* 1.3 59.5 + - - +
54E PRO 3.7 0.9 - - - -
55E THR* 3.5 9.1 + - - -
56E TRP* 3.4 22.2 + - - +
168E CYS* 3.8 2.0 - - - -
194E PRO* 5.8 1.3 - - + +
195E ASP 3.6 22.9 - - - +
196E GLY 3.8 11.7 - - - -
197E VAL* 3.9 9.9 - - + +
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Residues in contact with PHE 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ALA 3.0 14.5 + - - +
50E GLN* 3.8 22.9 - - - +
52E ALA* 1.3 76.1 - - - +
54E PRO* 1.3 73.2 - - + +
56E TRP 3.1 0.2 + - - -
57E ARG* 2.7 63.6 + - + +
138E PRO* 3.7 16.2 - - + -
139E MET 4.5 1.3 - - - -
140E GLY* 3.5 40.8 - - - -
141E VAL* 5.5 0.2 - - + -
166E GLY 3.4 25.4 - - - -
167E ASN* 4.4 2.2 - - - -
168E CYS* 3.5 11.0 - - + -
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Residues in contact with PRO 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLN* 3.4 15.0 - - - +
51E HIS 3.6 10.5 - - - +
52E ALA 3.8 0.2 - - - -
53E PHE* 1.3 104.5 - - + +
55E THR* 1.3 64.0 + - + +
57E ARG* 3.3 18.4 + - + +
58E ASN* 3.4 16.1 + - - +
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Residues in contact with THR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E HIS 5.4 1.5 + - - +
52E ALA* 3.5 11.8 + - - -
54E PRO* 1.3 81.2 - - + +
56E TRP* 1.3 66.5 + - - +
58E ASN* 3.2 7.7 + - - +
59E THR* 2.9 26.2 + - - -
194E PRO* 6.1 1.7 - - - +
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Residues in contact with TRP 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ALA 3.4 17.0 + - - +
53E PHE 3.1 3.5 + - - +
55E THR* 1.3 79.4 + - - +
57E ARG* 1.3 62.9 + - - +
59E THR* 3.2 29.3 + - + -
63E LYS* 5.4 0.9 - - + -
64E ARG* 3.1 60.1 + - + +
67E VAL* 4.2 10.1 - - + -
163E ILE* 2.9 38.0 + - + -
166E GLY 3.5 15.9 - - - -
167E ASN 3.1 23.5 + - - -
168E CYS* 4.2 1.6 - - - -
193E LEU* 3.7 13.7 - - + -
194E PRO* 3.8 30.1 - - + -
197E VAL* 3.4 22.6 - - + +
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Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 2.7 55.2 + - + +
54E PRO* 3.3 10.2 + - - +
56E TRP* 1.3 72.5 - - - +
58E ASN* 1.3 66.3 + - - +
64E ARG* 3.1 16.8 + - - +
137E GLN* 3.5 27.7 + - - +
138E PRO* 3.7 20.2 + - + +
166E GLY 3.7 10.6 + - - -
427F ASP* 3.5 24.9 + - - -
428F ASN* 3.1 31.3 - - - +
430F GLN* 3.9 19.4 - - - +
452F TRP* 5.4 1.2 - - - -
124H ARG* 3.4 29.4 + - - +
125H ASN* 4.7 0.2 + - - -
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Residues in contact with ASN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PRO 3.4 13.9 + - - +
55E THR* 3.2 8.2 + - - +
57E ARG* 1.3 89.9 + - - +
59E THR* 1.3 62.0 + - - +
60E PRO* 3.4 6.9 - - - +
423F ARG* 6.2 0.4 - - - -
427F ASP* 4.0 4.3 + - - +
428F ASN* 4.4 13.7 - - - +
124H ARG* 3.0 21.8 + - - -
125H ASN* 3.4 20.9 + - - +
128H PRO* 5.2 4.5 - - - +
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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