Contacts of the helix formed by residues 38 - 58 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLU* 2.9 33.9 + - - -
17H THR* 5.1 1.8 - - - -
18H ARG* 5.0 3.8 - - - +
36H LEU 3.8 0.8 + - - -
37H ALA* 1.3 74.6 - - - +
39H THR* 1.3 65.6 + - - +
40H LYS* 2.9 15.8 + - - +
41H THR 2.9 10.7 + - - -
42H VAL* 3.2 12.3 + - - +
206H GLU* 3.4 22.2 - - - -
327K GLN* 5.7 1.7 + - - -
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Residues in contact with THR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H SER* 1.3 74.8 - - - +
40H LYS* 1.3 58.6 + - - +
42H VAL* 3.9 1.8 - - - +
43H GLU* 3.0 42.4 + - - +
206H GLU* 3.7 23.5 + - + +
209H ASP* 6.2 0.7 - - + -
210H ALA* 3.8 31.6 - - + +
327K GLN* 5.4 4.7 + - - -
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Residues in contact with LYS 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLU* 5.3 2.0 - - + +
38H SER* 3.0 10.6 + - - +
39H THR* 1.3 82.5 + - - +
41H THR* 1.3 59.2 + - - +
43H GLU* 3.4 8.4 + - - +
44H GLN* 3.0 46.0 + - + +
327K GLN* 4.4 28.2 - - + +
330K GLU* 3.9 24.5 + - - -
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Residues in contact with THR 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H HIS* 3.8 16.6 - - + -
8H ILE* 3.6 25.0 - - + +
13H VAL* 5.1 2.9 - - + -
15H GLU* 2.5 40.8 + - + +
37H ALA* 3.8 17.7 - - + -
38H SER 2.9 5.3 + - - -
40H LYS* 1.3 75.8 - - - +
42H VAL* 1.3 66.3 + - - +
44H GLN* 3.4 18.5 + - - +
45H ALA* 3.2 14.2 + - - +
201H VAL* 4.1 1.7 - - + +
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ALA* 4.3 5.6 - - + -
38H SER 3.2 12.6 + - - +
39H THR 3.9 6.5 - - - +
41H THR* 1.3 75.2 - - - +
43H GLU* 1.3 54.1 + - + +
45H ALA* 2.7 26.0 + - - +
46H ILE* 2.9 30.1 + - + +
170H VAL* 5.3 1.1 - - + -
201H VAL* 4.2 20.9 - - + -
207H ALA* 3.9 34.3 - - + +
210H ALA* 3.8 19.5 - - + -
211H LEU* 3.9 20.6 - - + -
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Residues in contact with GLU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H THR* 3.0 32.8 + - - +
40H LYS* 3.6 7.8 - - - +
41H THR 3.4 0.2 - - - -
42H VAL* 1.3 74.9 - - + +
44H GLN* 1.3 57.7 + - - +
46H ILE* 4.4 5.6 - - + -
47H SER* 2.8 35.8 + - - +
210H ALA* 5.9 2.9 - - + +
214H ASP* 3.7 22.1 - - + +
216H ARG* 3.8 10.6 + - - +
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Residues in contact with GLN 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.1 17.2 - - + +
13H VAL* 5.2 5.7 - - - +
40H LYS* 3.0 43.4 + - + +
41H THR* 3.5 20.4 + - - +
42H VAL 3.2 0.2 - - - -
43H GLU* 1.3 75.7 - - - +
45H ALA* 1.3 57.0 + - - +
47H SER* 3.3 7.1 + - - -
48H ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 3.6 28.2 - - + +
41H THR 3.2 7.9 + - - +
42H VAL 2.7 15.1 + - - +
44H GLN* 1.3 72.2 - - - +
46H ILE* 1.3 64.9 + - - +
48H ALA* 3.2 3.6 + - - +
49H ALA* 2.9 22.7 + - - +
170H VAL* 4.1 22.9 - - + -
199H ASN* 4.0 12.2 + - + -
201H VAL* 4.3 6.7 - - + -
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Residues in contact with ILE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H VAL* 2.9 36.9 + - + +
43H GLU* 3.9 4.7 - - + +
45H ALA* 1.3 74.8 - - - +
47H SER* 1.3 57.6 + - - +
49H ALA* 3.1 8.1 + - - +
50H GLN* 2.8 27.5 + - - +
141H VAL* 4.6 6.3 - - + -
170H VAL* 4.3 8.1 - - + -
210H ALA 4.5 2.2 - - - +
211H LEU* 4.3 9.9 - - + -
214H ASP* 3.7 29.8 - - + +
216H ARG* 3.5 45.5 - - + +
217H VAL* 4.0 20.4 - - + -
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Residues in contact with SER 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLU* 2.8 22.4 + - - +
44H GLN* 3.5 7.7 - - - -
46H ILE* 1.3 75.2 - - - +
48H ALA* 1.3 58.7 + - - +
50H GLN* 3.8 2.8 - - - +
51H HIS* 3.0 30.0 + - - +
216H ARG* 2.8 27.4 + - - +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.1 9.4 - - + -
9H ASN* 3.9 36.6 - - + +
44H GLN 2.9 13.8 + - - +
45H ALA 3.2 8.9 + - - +
47H SER* 1.3 76.0 - - - +
49H ALA* 1.3 61.4 + - - +
51H HIS* 3.4 7.6 + - - +
52H ALA* 3.2 23.6 + - - +
196H GLY* 3.8 5.0 - - - +
199H ASN* 4.3 3.6 - - - +
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Residues in contact with ALA 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ALA 2.9 12.0 + - - +
46H ILE 3.3 8.1 - - - +
48H ALA* 1.3 74.5 - - - +
50H GLN* 1.3 64.9 + - - +
52H ALA 3.1 2.1 + - - -
53H PHE* 3.0 20.6 + - - +
141H VAL* 3.5 29.6 - - + -
168H CYS* 3.3 20.6 - - + -
170H VAL* 4.2 4.0 - - + -
196H GLY 3.3 15.2 + - - +
199H ASN* 4.0 6.3 - - - +
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Residues in contact with GLN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE 2.8 18.6 + - - +
47H SER* 3.8 8.1 - - - +
49H ALA* 1.3 72.6 - - - +
51H HIS* 1.3 61.1 + - - +
53H PHE* 3.5 22.9 + - - +
54H PRO* 3.3 22.0 - - - +
140H GLY* 5.6 1.1 - - - -
141H VAL* 3.6 21.7 + - + +
216H ARG* 3.8 35.7 - - - +
218H LYS* 5.6 1.6 - - - +
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Residues in contact with HIS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ASN* 5.8 7.0 - - - -
47H SER 3.0 17.8 + - - +
48H ALA* 3.7 7.6 - - - +
49H ALA 3.1 0.2 - - - -
50H GLN* 1.3 78.8 - - - +
52H ALA* 1.3 61.0 + - + +
54H PRO* 3.6 10.4 - - - +
55H THR* 5.2 1.9 + - - +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ASN* 5.4 0.2 - - - +
48H ALA 3.2 13.3 + - - +
49H ALA 3.1 5.3 + - - +
51H HIS* 1.3 78.1 - - + +
53H PHE* 1.3 63.4 + - - +
54H PRO* 3.6 0.7 - - - -
55H THR* 3.4 10.3 + - - -
56H TRP* 3.3 21.1 + - - +
168H CYS* 3.8 2.2 - - - -
194H PRO* 5.8 1.6 - - + -
195H ASP 3.6 24.7 - - - +
196H GLY 3.9 10.5 - - - -
197H VAL* 4.0 10.7 - - + +
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Residues in contact with PHE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G GLN* 6.4 0.2 - - - -
49H ALA 3.0 15.8 + - - +
50H GLN* 3.6 22.9 - - - +
52H ALA* 1.3 76.3 - - - +
54H PRO* 1.4 67.3 - - + +
56H TRP* 3.0 0.9 + - - -
57H ARG* 2.6 71.9 + - + +
138H PRO* 3.8 15.7 - - + -
139H MET 4.4 1.8 - - - -
140H GLY* 3.5 41.3 - - - -
141H VAL* 5.3 0.4 - - + -
166H GLY 3.4 24.2 - - - -
168H CYS* 3.4 13.7 - - + -
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Residues in contact with PRO 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H GLN* 3.3 18.2 - - - +
51H HIS 3.6 11.7 - - - +
52H ALA 3.7 0.7 - - - -
53H PHE* 1.4 100.1 - - + +
55H THR* 1.3 62.3 + - + +
57H ARG* 3.6 10.3 - - + +
58H ASN* 3.5 26.2 + - - -
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Residues in contact with THR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H HIS 5.2 1.3 + - - +
52H ALA* 3.4 13.2 + - - -
54H PRO* 1.3 78.5 - - + +
56H TRP* 1.3 58.8 + - - +
58H ASN* 3.6 5.2 + - - +
59H THR* 2.6 30.2 + - - -
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Residues in contact with TRP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H ALA 3.3 16.5 + - - +
53H PHE* 3.0 4.6 + - - +
55H THR* 1.3 79.3 + - - +
57H ARG* 1.3 66.2 - - - +
59H THR* 3.1 35.2 + - + -
63H LYS* 5.6 1.3 - - + -
64H ARG* 3.3 57.6 + - + +
67H VAL* 4.2 9.6 - - + -
163H ILE* 2.9 37.8 + - + -
166H GLY* 3.5 17.3 - - - -
167H ASN 3.1 23.9 + - - -
168H CYS* 4.4 0.9 - - - -
193H LEU* 3.7 13.2 - - + -
194H PRO* 3.7 31.4 - - + -
197H VAL* 3.6 22.0 - - + +
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Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ARG* 3.3 24.4 + - - +
427G ASP* 2.7 47.9 + - - -
428G ASN* 3.5 16.9 - - - +
430G GLN* 4.1 16.1 + - - +
452G TRP* 5.6 0.4 - - - -
53H PHE* 2.6 53.4 + - + +
54H PRO* 3.6 9.4 - - - +
56H TRP* 1.3 72.9 - - - +
58H ASN* 1.3 67.7 + - - +
59H THR 4.1 0.2 - - - +
64H ARG* 3.3 16.4 + - - +
137H GLN* 3.5 27.5 + - - +
138H PRO* 4.0 17.0 + - + +
166H GLY 3.9 10.8 + - - -
473H LYS* 6.2 0.4 - - - +
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Residues in contact with ASN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ARG* 3.3 18.8 + - - -
125E ASN* 3.6 21.3 + - - +
128E PRO* 5.0 6.8 - - - +
423G ARG* 6.2 0.9 - - - -
427G ASP* 4.1 5.0 + - - +
428G ASN* 4.5 10.3 + - - +
54H PRO 3.5 16.8 + - - +
55H THR* 3.6 6.3 + - - +
56H TRP 3.2 1.0 - - - -
57H ARG* 1.3 88.7 + - - +
59H THR* 1.3 64.6 + - - +
60H PRO* 3.5 6.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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