Contacts of the helix formed by residues 303 - 319 (chain B) in PDB entry 1ZUZ
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 ARG 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 5.8 4.4 - - - +
11A GLU* 3.5 34.9 + - - +
144A MET* 6.5 1.3 - - - -
148A LYS* 3.0 36.3 + - - +
302B ARG* 1.3 80.7 - - - +
304B ARG* 1.3 64.9 + - - +
305B TRP 3.4 2.7 - - - +
306B LYS* 3.6 48.2 - - + +
307B LEU* 3.0 23.5 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.6 24.3 + - - -
109A MET* 4.4 4.5 - - + -
114A GLU* 3.7 14.6 + - - +
115A LYS 4.2 9.3 + - - +
116A LEU* 3.6 36.8 - - - +
120A GLU* 3.0 29.8 + - + +
124A MET* 3.6 27.8 - - + -
302B ARG* 3.5 23.5 + - + +
303B ARG* 1.3 73.9 - - - +
305B TRP* 1.3 63.8 + - - +
307B LEU* 3.7 4.4 - - - +
308B ASP* 3.1 25.6 + - - +
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.5 31.4 - + - -
100A ILE* 3.7 24.9 - - + -
105A LEU* 3.6 19.7 - - + +
124A MET* 3.5 49.9 - - + +
125A ILE* 4.1 11.7 - - + -
128A ALA* 3.8 11.2 - - + -
136A VAL* 3.5 39.3 - - + -
141A PHE* 3.6 18.0 - + - -
144A MET* 4.6 16.4 - - + -
145A MET* 3.5 17.7 - - + -
303B ARG 3.4 0.4 - - - -
304B ARG* 1.3 79.9 - - - +
306B LYS* 1.3 58.4 + - - +
308B ASP* 3.4 2.6 + - + +
309B PHE* 2.7 30.0 + - + +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A MET 5.8 1.1 - - - +
145A MET* 3.5 39.3 - - + +
147A ALA 4.7 2.7 - - - +
148A LYS 4.0 11.0 - - - +
303B ARG* 3.4 57.2 + - + +
304B ARG 3.3 0.6 - - - -
305B TRP* 1.3 78.0 - - - +
307B LEU* 1.3 58.2 + - - +
309B PHE* 3.4 5.6 + - + +
310B SER* 2.8 35.7 + - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.4 44.2 - - + +
14A GLU* 3.3 25.6 - - + +
15A ALA* 4.4 12.3 - - + +
114A GLU* 3.8 9.4 - - - +
302B ARG* 5.2 1.8 - - - -
303B ARG* 3.0 18.7 + - - +
304B ARG* 3.7 5.2 - - - +
306B LYS* 1.3 76.9 - - - +
308B ASP* 1.3 76.8 + - - +
310B SER* 2.6 27.5 + - - +
311B ILE* 3.1 23.4 + - + +
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Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.2 4.9 - - - +
92A PHE* 4.2 15.3 - - + -
109A MET* 3.0 38.9 - - + +
112A LEU* 4.1 14.8 - - + +
114A GLU* 2.7 31.0 - - - +
304B ARG 3.1 16.1 + - - +
305B TRP* 4.0 4.9 - - + +
307B LEU* 1.3 78.7 - - - +
309B PHE* 1.3 66.5 + - - +
311B ILE* 3.1 7.6 + - - +
312B VAL* 3.0 25.3 + - - +
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 4.7 7.0 - - + -
77A LYS* 6.3 2.2 - - - -
80A ASP* 4.4 15.9 - - + -
85A ILE* 4.7 17.0 - - + -
88A ALA* 3.7 24.5 - - + -
92A PHE* 4.1 12.3 - + + -
141A PHE* 3.7 27.8 - + - -
145A MET* 3.8 32.1 - - + -
305B TRP* 2.7 25.7 + - + +
306B LYS* 3.5 8.3 - - + +
308B ASP* 1.3 71.5 - - - +
310B SER* 1.3 56.5 + - - +
312B VAL* 3.2 1.9 + - - +
313B SER* 2.8 56.0 + - - -
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 5.5 1.2 - - - +
72A MET* 3.6 17.3 - - - +
76A MET* 3.0 27.6 - - - +
306B LYS* 2.8 20.3 + - - -
307B LEU* 2.6 25.0 + - - +
309B PHE* 1.3 78.7 - - - +
311B ILE* 1.3 59.8 + - - +
313B SER* 2.9 9.2 + - - -
314B LEU* 2.8 26.8 + - - +
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.9 18.8 - - + +
18A LEU* 3.1 36.8 - - + -
19A PHE* 4.1 24.9 - - + -
35A VAL* 4.6 1.8 - - + -
72A MET* 5.7 3.6 - - - -
112A LEU* 3.9 26.5 - - + -
307B LEU* 3.1 26.1 + - + +
308B ASP* 3.6 9.4 - - - +
310B SER* 1.3 83.1 + - - +
312B VAL* 1.3 64.8 + - - +
314B LEU* 3.5 6.8 + - + +
315B CYS* 3.1 27.6 + - - -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.9 24.9 - - + -
88A ALA* 3.6 34.5 - - + +
91A VAL* 3.8 28.9 - - + -
92A PHE* 4.1 21.1 - - + -
108A VAL* 4.8 0.9 - - + -
112A LEU* 4.6 8.1 - - + -
308B ASP 3.0 16.3 + - - +
309B PHE 3.6 7.0 - - - +
311B ILE* 1.3 75.5 - - - +
313B SER* 1.3 62.7 + - - +
315B CYS* 3.4 1.7 + - - +
316B ASN* 3.0 27.8 + - - +
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Residues in contact with SER 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A MET* 3.0 22.9 - - - +
80A ASP* 3.8 22.2 - - - -
84A GLU 6.0 0.9 - - - -
88A ALA* 5.0 2.4 - - - +
309B PHE* 2.8 34.8 + - - -
310B SER* 2.9 15.6 + - - -
312B VAL* 1.3 74.9 - - - +
314B LEU* 1.3 54.6 + - - +
316B ASN* 3.4 8.7 + - - +
317B HIS* 2.9 37.7 + - - -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.0 29.4 - - + -
68A PHE* 4.4 1.1 - - + -
71A MET* 4.0 35.4 - - + +
72A MET* 3.9 19.1 - - - -
75A LYS* 3.5 40.8 - - + +
76A MET* 4.2 8.7 - - + -
310B SER 2.8 18.6 + - - +
311B ILE* 3.6 5.2 - - - +
313B SER* 1.3 76.9 + - - +
315B CYS* 1.3 51.8 + - - +
317B HIS* 2.9 5.4 + - - +
318B LEU* 2.8 47.4 + - + +
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Residues in contact with CYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.1 14.6 - - - -
35A VAL* 3.9 20.9 - - - -
36A MET* 4.0 21.6 - - + +
39A LEU* 3.9 24.5 - - + -
41A GLN* 3.0 21.3 - - - +
311B ILE 3.1 18.3 + - - +
312B VAL 3.8 3.6 - - - +
313B SER 3.3 0.2 - - - -
314B LEU* 1.3 79.3 - - - +
316B ASN* 1.3 65.3 + - - +
318B LEU* 3.4 10.1 + - - +
319B THR* 3.3 16.1 + - - +
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Residues in contact with ASN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.5 3.8 - - - +
41A GLN* 4.0 16.0 + - - +
84A GLU* 4.2 9.2 + - + +
87A GLU* 3.4 44.8 + - - +
88A ALA* 3.7 17.2 - - - +
91A VAL* 4.8 6.5 - - - +
312B VAL* 3.0 22.7 + - - +
313B SER* 3.6 7.1 - - - +
315B CYS* 1.3 77.1 - - - +
317B HIS* 1.3 60.4 + - + +
319B THR* 3.1 26.0 + - - +
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.5 38.6 + - + +
76A MET* 5.3 1.3 - - + -
78A ASP* 3.8 35.6 + - + +
80A ASP* 3.5 37.2 - - - -
84A GLU* 3.7 25.4 + - + -
313B SER* 2.9 25.6 + - - -
314B LEU 2.9 7.6 + - - +
316B ASN* 1.3 77.5 - - + +
318B LEU* 1.3 62.6 + - - +
319B THR 3.5 0.2 + - - -
320B ARG* 3.7 19.8 + - - +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.4 7.6 - - + -
36A MET* 3.1 35.9 - - + -
51A MET* 3.7 39.2 - - + +
54A GLU* 5.7 0.7 - - - +
71A MET* 4.1 26.5 - - + -
75A LYS* 4.2 29.7 + - + +
314B LEU* 2.8 42.4 + - + +
315B CYS* 3.7 2.0 - - - +
316B ASN 3.3 0.2 - - - -
317B HIS* 1.3 69.6 - - - +
319B THR* 1.3 61.5 + - - +
320B ARG* 2.8 13.2 + - - +
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 4.6 7.4 - - - -
41A GLN* 2.8 52.0 + - + +
42A ASN 5.9 0.2 - - - +
43A PRO* 4.8 8.5 - - + -
51A MET* 4.3 16.6 - - + -
315B CYS 3.3 3.0 + - - +
316B ASN 3.1 16.6 + - - +
317B HIS 3.4 0.2 - - - -
318B LEU* 1.3 71.5 - - - +
320B ARG* 1.3 65.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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