Contacts of the helix formed by residues 38 - 58 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU* 2.7 34.7 + - - -
17F THR* 4.9 2.7 - - - -
18F ARG* 5.4 0.4 - - - +
36F LEU 3.6 0.6 + - - -
37F ALA* 1.3 74.7 - - - +
39F THR* 1.3 65.2 + - - +
40F LYS* 3.4 15.5 + - - +
41F THR* 3.1 14.6 + - - -
42F VAL* 3.1 14.6 + - - +
206F GLU* 3.2 22.9 - - - -
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Residues in contact with THR 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 1.3 76.0 - - - +
40F LYS* 1.3 58.2 + - - +
42F VAL* 3.7 2.1 + - - +
43F GLU* 3.0 45.7 + - - +
206F GLU* 3.2 35.2 + - + +
209F ASP* 6.1 0.9 - - + -
210F ALA* 3.9 22.1 - - + +
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Residues in contact with LYS 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 3.1 10.8 + - - +
39F THR* 1.3 80.8 + - - +
41F THR* 1.3 63.2 - - - +
43F GLU* 3.5 14.0 + - - +
44F GLN* 3.2 41.5 + - + +
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Residues in contact with THR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F HIS* 3.7 29.4 - - + -
8F ILE* 3.8 17.3 - - + +
13F VAL* 5.2 2.7 - - + -
15F GLU* 3.0 34.0 + - + +
37F ALA* 3.8 12.8 - - + -
38F SER* 3.1 8.1 + - - -
40F LYS* 1.3 76.6 - - - +
42F VAL* 1.3 65.5 + - - +
44F GLN* 3.0 26.0 + - - +
45F ALA 3.1 9.4 + - - -
201F VAL* 4.2 1.8 - - + -
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Residues in contact with VAL 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA* 4.4 2.0 - - + -
38F SER 3.1 12.3 + - - +
39F THR 3.9 7.2 - - - +
41F THR* 1.3 75.5 - - - +
43F GLU* 1.3 56.8 + - + +
45F ALA* 2.9 24.4 + - - +
46F ILE* 2.9 32.9 + - + +
170F VAL* 5.1 0.9 - - + -
201F VAL* 3.8 28.3 - - + -
207F ALA* 3.9 26.7 - - + +
210F ALA* 3.8 19.1 - - + -
211F LEU* 3.8 19.1 - - + -
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F THR* 3.0 36.8 + - - +
40F LYS* 3.6 12.4 - - - +
41F THR 3.3 0.2 - - - -
42F VAL* 1.3 76.6 - - + +
44F GLN* 1.3 53.3 + - - +
46F ILE* 4.4 4.5 - - + -
47F SER* 2.8 38.4 + - - +
210F ALA* 5.7 2.8 - - + +
214F ASP* 3.8 19.7 - - - +
216F ARG* 3.6 13.3 + - - +
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Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 3.8 19.7 - - + +
13F VAL* 5.4 5.7 - - - +
40F LYS* 3.2 36.3 + - + +
41F THR* 3.0 18.8 + - - +
43F GLU* 1.3 76.6 - - - +
45F ALA* 1.3 54.8 + - - +
47F SER* 3.4 6.5 + - - -
48F ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 4.0 26.8 - - + +
41F THR 3.1 9.3 + - - +
42F VAL* 2.9 13.8 + - - +
44F GLN* 1.3 76.7 - - - +
46F ILE* 1.3 56.9 - - - +
48F ALA* 3.5 1.4 - - - +
49F ALA* 3.0 24.3 + - - +
170F VAL* 4.1 24.0 - - + -
199F ASN* 3.4 19.0 + - + -
201F VAL* 4.5 6.5 - - + -
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F VAL* 2.9 40.8 + - + +
43F GLU* 3.9 5.8 - - + +
45F ALA* 1.3 72.6 - - - +
47F SER* 1.3 59.0 + - - +
49F ALA* 3.2 6.5 + - - +
50F GLN* 2.8 29.5 + - - +
141F VAL* 4.7 6.3 - - + -
170F VAL* 4.3 12.3 - - + -
210F ALA 4.8 0.9 - - - +
211F LEU* 4.1 6.5 - - + -
214F ASP* 3.8 29.4 - - + +
216F ARG* 3.3 43.3 - - + +
217F VAL* 3.9 20.2 - - + -
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLU* 2.8 27.8 + - - +
44F GLN* 3.7 7.4 - - - -
45F ALA 3.4 0.2 - - - -
46F ILE* 1.3 74.0 - - - +
48F ALA* 1.3 53.8 + - - +
50F GLN* 3.8 2.8 - - - +
51F HIS* 2.9 35.9 + - - +
216F ARG* 2.8 24.0 + - - +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 4.2 3.1 - - + -
9F ASN* 3.2 39.6 - - + +
44F GLN 3.0 17.1 + - - +
45F ALA 3.5 5.6 - - - +
47F SER* 1.3 74.2 - - - +
49F ALA* 1.3 65.2 + - - +
51F HIS* 3.4 5.5 + - - +
52F ALA* 3.1 24.6 + - - +
196F GLY* 4.0 3.5 - - - +
199F ASN* 4.1 11.9 - - - +
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Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA 3.0 14.5 + - - +
46F ILE 3.4 8.5 - - - +
48F ALA* 1.3 75.0 - - - +
50F GLN* 1.3 63.5 + - - +
52F ALA* 3.2 2.8 + - - +
53F PHE* 3.1 18.0 + - - +
141F VAL* 3.5 28.9 - - + -
168F CYS* 3.2 22.1 - - + -
169F PHE 4.6 0.4 - - - +
170F VAL* 4.1 3.6 - - + -
196F GLY 3.5 11.9 - - - -
199F ASN* 3.7 10.0 - - - +
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Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ILE 2.8 19.7 + - - +
47F SER* 3.9 4.0 - - - +
49F ALA* 1.3 73.6 - - - +
51F HIS* 1.3 63.7 + - - +
53F PHE* 3.4 23.4 + - - +
54F PRO* 3.2 22.4 - - - +
140F GLY* 5.3 2.5 - - - -
141F VAL* 3.2 26.0 + - + +
216F ARG* 3.8 36.0 - - + +
218F LYS* 5.5 1.6 - - - +
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Residues in contact with HIS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASN* 5.4 7.4 - - - -
47F SER 2.9 19.5 + - - +
48F ALA* 3.7 6.7 - - - +
49F ALA 3.3 0.2 - - - -
50F GLN* 1.3 77.4 - - - +
52F ALA* 1.3 60.2 + - - +
54F PRO* 3.5 11.0 - - - +
55F THR* 5.5 1.2 + - - +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASN* 5.8 0.2 - - - +
48F ALA 3.1 16.7 + - - +
49F ALA 3.2 4.9 + - - +
51F HIS* 1.3 77.6 - - + +
53F PHE* 1.3 63.4 + - - +
54F PRO* 3.7 0.4 - - - -
55F THR* 3.7 8.7 + - - -
56F TRP* 3.4 21.0 + - - +
168F CYS* 3.8 4.7 - - - -
194F PRO* 5.8 1.7 - - + +
195F ASP 3.7 22.2 - - - +
196F GLY 3.9 12.1 - - - -
197F VAL* 3.9 8.1 - - + +
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Residues in contact with PHE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ALA 3.1 6.3 + - - +
50F GLN* 3.5 27.1 - - - +
52F ALA* 1.3 74.3 - - - +
54F PRO* 1.3 71.8 - - + +
56F TRP* 3.0 1.1 + - - -
57F ARG* 2.7 65.1 + - + +
138F PRO* 3.9 14.6 - - + -
139F MET 4.2 2.7 - - - -
140F GLY* 3.5 45.8 - - - +
166F GLY 3.3 25.8 - - - -
167F ASN* 4.3 0.2 - - - -
168F CYS* 3.4 17.9 - - + -
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Residues in contact with PRO 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLN* 3.2 17.7 - - - +
51F HIS* 3.5 11.9 - - - +
52F ALA 3.8 0.4 - - - -
53F PHE* 1.3 101.1 - - + +
55F THR* 1.3 61.9 + - + +
57F ARG* 3.6 8.6 - - + +
58F ASN* 3.5 26.0 + - - +
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Residues in contact with THR 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F HIS 5.5 0.9 + - - +
52F ALA* 3.7 9.6 + - - -
53F PHE 3.2 0.4 - - - -
54F PRO* 1.3 79.5 - - + +
56F TRP* 1.3 61.8 + - - +
57F ARG 3.2 0.2 - - - -
58F ASN* 3.4 5.7 + - - +
59F THR* 2.9 28.2 + - - -
194F PRO* 6.1 1.2 - - - +
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Residues in contact with TRP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ALA 3.4 17.0 + - - +
53F PHE* 3.0 5.7 + - - +
55F THR* 1.3 80.2 + - - +
57F ARG* 1.3 66.1 + - - +
59F THR* 3.4 29.0 - - + -
63F LYS* 5.8 1.3 - - + -
64F ARG* 3.3 56.3 + - + +
67F VAL* 4.1 11.2 - - + -
163F ILE* 2.9 39.8 + - + -
166F GLY 3.7 10.8 - - - -
167F ASN 3.1 23.8 + - - -
168F CYS* 4.4 1.3 - - - -
193F LEU* 3.6 14.1 - - + -
194F PRO* 3.6 32.8 - - + -
197F VAL* 3.5 21.9 - - + +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ASP* 2.8 32.7 + - - -
428E ASN* 3.4 27.5 - - - +
430E GLN* 4.1 17.5 - - - +
452E TRP* 5.3 1.0 - - - -
53F PHE* 2.7 49.4 + - + +
54F PRO* 3.6 9.6 - - - +
56F TRP* 1.3 73.0 - - - +
58F ASN* 1.3 67.7 + - - +
59F THR 3.6 0.3 - - - +
64F ARG* 3.0 19.8 + - - +
137F GLN* 3.4 29.3 + - - +
138F PRO* 4.0 21.2 + - + +
166F GLY 3.8 10.7 + - - -
473F LYS* 6.3 0.2 - - - +
124G ARG* 3.5 21.4 + - - +
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Residues in contact with ASN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ASP* 4.2 5.3 + - - +
428E ASN* 4.3 14.1 - - - +
54F PRO 3.5 15.4 + - - +
55F THR* 3.4 7.4 + - - +
56F TRP 3.3 0.2 - - - -
57F ARG* 1.3 85.3 + - - +
59F THR* 1.3 63.9 + - - +
60F PRO* 3.5 6.8 - - - +
124G ARG* 3.2 20.6 + - - -
125G ASN* 3.7 17.3 + - - +
128G PRO* 5.3 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