Contacts of the helix formed by residues 38 - 58 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLU* 2.6 34.0 + - - -
17G THR* 5.1 2.7 - - - -
18G ARG* 4.9 2.5 - - - +
36G LEU 3.8 0.2 + - - -
37G ALA* 1.3 77.1 - - - +
39G THR* 1.3 66.5 + - - +
40G LYS* 3.3 17.2 + - - +
41G THR* 3.0 10.8 + - - -
42G VAL* 3.2 12.3 + - - +
206G GLU* 3.2 22.2 - - - -
327J GLN* 4.0 9.9 + - - -
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Residues in contact with THR 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G SER* 1.3 75.7 - - - +
40G LYS* 1.3 65.1 + - - +
42G VAL* 3.3 1.8 + - - +
43G GLU* 3.0 40.3 + - - +
206G GLU* 3.4 24.9 + - + +
209G ASP* 6.1 0.7 - - + -
210G ALA* 3.9 31.1 - - + +
327J GLN* 5.5 1.4 + - - -
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Residues in contact with LYS 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLU* 5.2 1.1 - - - +
38G SER* 3.2 5.7 + - - +
39G THR* 1.3 83.6 + - - +
41G THR* 1.3 58.8 + - - +
43G GLU* 3.7 12.7 + - - +
44G GLN* 3.4 42.2 + - + +
327J GLN* 3.2 46.0 + - + +
330J GLU* 2.7 31.3 + - - +
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Residues in contact with THR 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G HIS* 4.0 17.9 - - + +
8G ILE* 3.7 22.7 - - + +
13G VAL* 5.4 2.2 - - + -
14G THR 6.2 0.2 - - - -
15G GLU* 3.1 35.1 + - + +
37G ALA* 3.7 20.2 - - + -
38G SER 3.0 8.8 + - - -
40G LYS* 1.3 76.6 - - - +
42G VAL* 1.3 63.6 + - - +
44G GLN* 3.4 15.7 + - - +
45G ALA* 3.3 15.8 + - - +
201G VAL* 4.2 2.2 - - + -
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Residues in contact with VAL 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ALA* 4.3 3.6 - - + -
38G SER 3.2 11.5 + - - +
39G THR 3.3 2.0 + - - +
41G THR* 1.3 76.4 - - - +
43G GLU* 1.3 58.8 + - - +
45G ALA* 3.0 5.5 + - - +
46G ILE* 2.8 44.1 + - + +
170G VAL* 5.2 0.9 - - + -
201G VAL* 3.8 26.9 - - + -
207G ALA* 3.8 29.8 - - + +
210G ALA* 3.6 26.0 - - + -
211G LEU* 3.8 18.6 - - + -
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Residues in contact with GLU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G THR* 3.0 34.9 + - - +
40G LYS* 3.8 10.7 - - - +
41G THR 3.4 0.2 - - - -
42G VAL* 1.3 77.5 - - + +
44G GLN* 1.3 49.5 + - - +
46G ILE* 4.3 4.3 - - + -
47G SER* 2.7 42.2 + - - +
210G ALA* 5.8 2.4 - - + +
214G ASP* 3.8 19.2 - - - +
216G ARG* 3.6 10.9 + - - +
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 4.0 19.2 - - + +
13G VAL* 5.5 3.6 - - - +
40G LYS* 3.4 37.7 + - + +
41G THR* 3.4 14.9 + - - +
42G VAL 3.2 0.8 - - - -
43G GLU* 1.3 72.8 - - - +
45G ALA* 1.3 60.4 + - - +
47G SER* 3.3 6.8 + - - -
48G ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 3.9 25.9 - - + +
41G THR 3.3 9.1 + - - +
42G VAL 3.0 10.2 + - - +
44G GLN* 1.3 77.7 - - - +
46G ILE* 1.3 62.5 + - - +
48G ALA* 3.1 5.2 + - - +
49G ALA* 3.0 20.1 + - - +
170G VAL* 4.1 25.8 - - + -
199G ASN* 3.6 14.0 + - + -
201G VAL* 4.2 9.2 - - + -
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Residues in contact with ILE 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 VAL* 2.8 40.2 + - + +
43G GLU* 3.8 5.4 - - + +
45G ALA* 1.3 72.5 - - - +
47G SER* 1.3 61.6 + - - +
49G ALA* 3.5 3.6 + - - +
50G GLN* 3.0 21.3 + - - +
141G VAL* 4.3 6.2 - - + +
170G VAL* 4.3 12.1 - - + -
210G ALA 4.4 2.2 - - - +
211G LEU* 4.0 12.1 - - + -
214G ASP* 3.6 29.4 - - + +
216G ARG* 3.4 42.0 - - + +
217G VAL* 3.7 22.2 - - + -
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Residues in contact with SER 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G GLU* 2.7 25.5 + - - +
44G GLN* 3.6 7.8 - - - -
46G ILE* 1.3 74.1 - - - +
48G ALA* 1.3 53.0 + - - +
50G GLN* 3.2 3.6 + - - +
51G HIS* 2.8 35.9 + - - +
216G ARG* 2.6 28.2 + - - +
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 4.2 4.9 - - + -
9G ASN* 3.7 41.7 - - + +
44G GLN 2.9 16.2 + - - +
45G ALA 3.1 5.4 + - - +
47G SER* 1.3 76.8 - - - +
49G ALA* 1.3 56.3 - - - +
51G HIS* 3.5 7.0 + - - +
52G ALA* 3.1 28.2 + - - +
196G GLY* 3.7 7.0 - - - +
199G ASN* 4.2 4.0 - - - +
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Residues in contact with ALA 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 ALA 3.0 11.8 + - - +
46G ILE 3.6 9.0 - - - +
48G ALA* 1.3 74.9 - - - +
50G GLN* 1.3 64.2 + - - +
52G ALA 3.2 1.2 + - - -
53G PHE* 3.1 20.3 + - - +
141G VAL* 3.8 20.9 - - + -
168G CYS* 3.3 26.5 - - + -
169G PHE 4.6 0.7 - - - +
170G VAL* 4.3 4.7 - - + -
196G GLY 3.2 12.3 + - - -
199G ASN* 3.7 11.4 - - - +
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Residues in contact with GLN 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE 3.0 17.3 + - - +
47G SER* 3.2 6.9 + - - +
49G ALA* 1.3 76.8 - - - +
51G HIS* 1.3 62.2 + - - +
53G PHE* 3.4 21.7 + - - +
54G PRO* 3.2 22.9 - - - +
140G GLY* 5.6 1.2 - - - -
141G VAL* 3.3 22.3 + - + +
216G ARG* 3.7 36.6 - - - +
218G LYS* 5.6 1.2 - - - +
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Residues in contact with HIS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ASN* 5.5 5.6 - - - -
47G SER 2.8 17.1 + - - +
48G ALA* 3.7 9.6 - - - +
49G ALA 3.2 0.2 - - - -
50G GLN* 1.3 79.0 - - - +
52G ALA* 1.3 59.8 + - + +
53G PHE 3.6 0.3 + - - -
54G PRO* 3.7 9.9 - - - +
55G THR* 5.4 1.6 + - - +
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Residues in contact with ALA 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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9G ASN* 5.6 0.2 - - - +
48G ALA 3.1 18.3 + - - +
49G ALA 3.2 4.4 + - - +
51G HIS* 1.3 76.7 - - + +
53G PHE* 1.3 61.4 + - - +
54G PRO 3.6 0.9 - - - -
55G THR* 3.7 9.7 + - - -
56G TRP* 3.3 23.9 + - - +
168G CYS* 3.9 2.5 - - - -
194G PRO* 6.0 0.9 - - + -
195G ASP 3.6 22.7 - - - +
196G GLY 3.9 11.2 - - - -
197G VAL* 4.0 9.6 - - + +
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Residues in contact with PHE 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 ALA 3.1 15.2 + - - +
50G GLN* 3.6 22.2 - - - +
52G ALA* 1.3 76.3 - - - +
54G PRO* 1.3 71.8 - - + +
56G TRP* 4.5 0.7 - - - -
57G ARG* 2.7 63.5 + - + +
138G PRO* 3.8 11.0 - - + -
139G MET 4.3 3.4 - - - -
140G GLY* 3.2 48.9 - - - -
166G GLY 3.3 26.2 - - - -
168G CYS* 3.6 11.9 - - + -
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Residues in contact with PRO 54 (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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50G GLN* 3.2 17.5 - - - +
51G HIS 3.7 11.4 - - - +
52G ALA 3.8 0.2 - - - -
53G PHE* 1.3 101.3 - - + +
55G THR* 1.3 65.4 + - + +
57G ARG* 3.5 10.0 + - + +
58G ASN* 3.4 25.3 + - - +
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Residues in contact with THR 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 HIS 5.4 1.3 + - - +
52G ALA* 3.7 10.3 + - - -
53G PHE 3.4 0.4 - - - -
54G PRO* 1.3 78.7 - - + +
56G TRP* 1.3 59.8 + - - +
58G ASN* 3.3 6.9 + - - +
59G THR* 2.7 30.4 + - - -
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Residues in contact with TRP 56 (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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52G ALA 3.3 18.2 + - - +
53G PHE* 3.9 2.9 - - - +
55G THR* 1.3 79.7 + - - +
57G ARG* 1.3 63.8 + - - +
59G THR* 3.1 37.6 + - + -
63G LYS* 5.5 0.9 - - + -
64G ARG* 3.4 55.8 + - + +
67G VAL* 4.2 10.5 - - + -
163G ILE* 2.9 42.4 + - + +
166G GLY 3.6 17.3 - - - -
167G ASN 3.4 23.3 + - - -
168G CYS* 4.4 0.9 - - - -
193G LEU* 3.6 13.2 - - + -
194G PRO* 3.6 33.2 - - + -
197G VAL* 3.9 16.6 - - + +
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Residues in contact with ARG 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ARG* 3.4 30.6 + - - +
53G PHE* 2.7 49.8 + - + +
54G PRO* 3.5 8.3 - - - +
56G TRP* 1.3 74.0 - - - +
58G ASN* 1.3 69.0 + - - +
64G ARG* 3.3 15.7 + - - +
137G GLN* 3.5 21.2 + - - +
138G PRO* 3.8 28.1 + - + +
166G GLY 3.9 10.2 + - - -
473G LYS* 6.2 0.4 - - - +
427H ASP* 2.8 26.7 + - - -
428H ASN* 3.4 26.4 - - - +
430H GLN* 4.3 15.3 + - - +
452H TRP* 5.5 0.8 - - - -
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Residues in contact with ASN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ARG* 3.1 21.7 + - - -
125F ASN* 3.6 19.2 + - - +
128F PRO* 5.4 3.6 - - - +
54G PRO 3.4 14.8 + - - +
55G THR* 3.3 8.2 + - - +
56G TRP 3.2 0.6 - - - -
57G ARG* 1.3 87.5 + - - +
59G THR* 1.3 61.9 + - - +
60G PRO* 3.5 7.3 - - - +
423H ARG* 6.2 0.2 - - - -
427H ASP* 3.9 6.7 + - - +
428H ASN* 4.3 13.5 + - - +
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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