Contacts of the helix formed by residues 80 - 98 (chain L) in PDB entry 1ZUM
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 ASP 80 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147I ASP* 3.4 33.8 - - - +
148I GLY* 2.9 17.1 + - - -
498I LYS* 2.7 31.0 + - - +
127J LYS* 5.2 2.8 + - - -
78L ARG 3.5 2.6 + - - +
79L MET* 1.3 79.6 - - - +
81L ALA* 1.3 56.9 + - - +
82L SER* 3.9 6.5 + - - +
83L HIS* 2.7 29.2 + - + +
84L ARG* 3.2 9.4 + - - +
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Residues in contact with ALA 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I PRO* 4.0 23.5 + - + +
147I ASP* 5.9 0.2 - - - +
498I LYS* 4.9 3.6 - - - +
79L MET 3.6 2.0 + - - -
80L ASP* 1.3 71.1 - - - +
82L SER* 1.3 63.3 + - - +
84L ARG* 3.1 35.6 + - - +
85L GLY 3.3 7.4 + - - -
136L ALA* 3.3 32.4 - - - +
137L ASP* 3.9 14.4 - - + -
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I PRO 5.1 0.6 + - - -
147I ASP* 2.7 34.1 + - - -
127J LYS* 5.5 3.4 + - - +
462J GLN* 4.5 2.0 - - - -
80L ASP* 3.9 3.5 - - - +
81L ALA* 1.3 79.9 - - - +
83L HIS* 1.3 59.3 + - - +
85L GLY* 3.3 4.6 + - - +
86L ARG* 3.1 30.1 + - - +
137L ASP* 3.5 30.0 - - - +
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Residues in contact with HIS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L MET* 3.3 37.7 - - + -
80L ASP* 2.7 27.3 + - + +
82L SER* 1.3 74.5 + - - +
84L ARG* 1.3 62.7 + - - +
85L GLY 3.0 1.8 - - - -
86L ARG* 2.9 33.4 + - + +
87L LEU* 2.9 29.7 + - + +
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Residues in contact with ARG 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500I SER* 3.6 28.3 - - - +
76L TRP* 3.7 33.3 + - + -
79L MET* 4.2 17.5 + - + -
80L ASP 3.2 9.1 + - - +
81L ALA* 3.1 25.8 + - - +
83L HIS* 1.3 75.0 - - - +
85L GLY* 1.3 62.5 + - - +
87L LEU* 3.3 4.6 + - - +
88L LEU* 3.1 27.1 + - - +
136L ALA* 3.3 22.4 + - + -
183L LEU 3.5 15.0 - - - +
184L ALA* 2.8 26.6 + - - -
185L THR* 3.8 9.4 + - - +
186L GLY* 3.4 19.8 - - - +
213L PHE* 4.9 1.2 - - - -
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Residues in contact with GLY 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L ALA 3.3 6.5 + - - -
82L SER* 3.6 5.8 - - - -
83L HIS 3.0 0.8 - - - -
84L ARG* 1.3 78.3 - - - +
86L ARG* 1.3 65.1 + - - +
88L LEU* 3.3 0.9 + - - -
89L ASN* 3.0 31.3 + - - -
133L ALA* 3.4 31.8 - - - +
136L ALA* 3.6 6.9 - - - +
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Residues in contact with ARG 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J ASN* 5.1 2.8 + - - -
93J ASP* 4.8 3.8 + - - -
96J GLU* 5.1 1.0 + - - -
130J ARG* 3.6 57.1 - - - +
82L SER* 3.1 21.5 + - - +
83L HIS* 2.9 30.8 + - + +
85L GLY* 1.3 75.4 - - - +
87L LEU* 1.3 58.5 + - - +
89L ASN* 3.2 34.9 + - - +
90L ARG* 2.9 29.2 + - - +
93L ASP* 6.0 0.2 + - - -
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Residues in contact with LEU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L TRP* 3.9 14.6 - - + -
79L MET* 3.5 35.9 - - + -
83L HIS* 2.9 25.6 + - + +
84L ARG 3.6 6.3 - - - +
86L ARG* 1.3 75.1 - - - +
88L LEU* 1.3 60.7 + - - +
90L ARG* 3.0 7.2 + - + +
91L LEU* 2.8 28.8 + - - +
211L ALA* 3.3 26.6 - - - +
212L GLY* 3.9 15.3 - - - +
213L PHE* 3.5 33.6 - - + +
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Residues in contact with LEU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L TRP* 6.4 0.2 - - + -
84L ARG 3.1 19.4 + - - +
85L GLY* 3.3 2.0 + - - +
87L LEU* 1.3 74.8 - - - +
89L ASN* 1.3 58.1 + - - +
91L LEU* 3.3 7.5 + - + +
92L ALA* 3.0 27.7 + - - +
129L LEU* 4.1 33.9 - - + +
132L TYR 4.1 0.9 - - - -
133L ALA* 3.7 35.4 - - + +
180L GLY* 4.1 9.2 - - - +
183L LEU* 4.1 29.2 - - + -
184L ALA* 3.9 34.3 - - + +
213L PHE* 4.2 7.4 - - + -
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Residues in contact with ASN 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG* 5.1 2.1 + - - -
89J ASN* 5.0 17.3 + - - +
85L GLY 3.0 18.7 + - - +
86L ARG* 3.6 32.7 - - - +
88L LEU* 1.3 79.1 - - - +
90L ARG* 1.3 56.1 + - - +
92L ALA* 3.4 5.1 + - - +
93L ASP* 3.0 37.5 + - - +
130L ARG* 3.7 24.8 + - - +
133L ALA* 3.5 21.0 - - - +
134L GLY* 5.3 0.4 - - - +
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Residues in contact with ARG 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ARG 2.9 12.6 + - - +
87L LEU* 3.3 13.5 - - + +
89L ASN* 1.3 75.3 - - - +
91L LEU* 1.3 64.6 + - - +
93L ASP* 3.2 21.7 + - - +
94L LEU* 3.0 56.8 + - + +
97L ARG* 5.6 0.4 - - - +
210L GLU* 4.6 12.3 + - - +
211L ALA* 3.7 30.4 + - + +
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Residues in contact with LEU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L LEU 2.8 13.1 + - - +
88L LEU* 3.5 12.3 - - + +
90L ARG* 1.3 77.1 - - - +
92L ALA* 1.3 63.3 + - - +
94L LEU* 3.1 5.7 + - - +
95L ILE* 3.0 31.0 + - + +
129L LEU* 4.1 28.5 - - + -
179L LEU* 4.8 8.5 - - + -
183L LEU* 5.3 1.1 - - + -
204L VAL* 4.3 3.8 - - + +
207L LEU* 3.7 16.8 - - + +
208L ILE* 3.6 52.0 - - + +
211L ALA* 4.0 5.1 - - + +
213L PHE* 4.2 17.3 - - + -
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Residues in contact with ALA 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L LEU 3.0 14.2 + - - +
89L ASN 3.6 8.3 - - - +
90L ARG 3.2 0.2 - - - -
91L LEU* 1.3 76.3 - - - +
93L ASP* 1.3 56.8 + - - +
95L ILE* 3.3 1.2 + - - -
96L GLU* 2.9 24.6 + - - +
126L LEU* 3.1 20.5 - - + +
129L LEU* 4.1 19.0 - - + +
130L ARG* 3.6 37.5 - - + +
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Residues in contact with ASP 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG* 4.9 3.6 + - - -
86L ARG* 6.0 0.2 + - - -
89L ASN* 3.0 25.1 + - - +
90L ARG* 3.2 24.6 + - - +
92L ALA* 1.3 75.7 - - - +
94L LEU* 1.3 58.9 + - - +
96L GLU* 3.4 4.5 + - - +
97L ARG* 3.0 26.2 + - - +
130L ARG* 3.0 23.6 + - - +
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Residues in contact with LEU 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L ARG* 3.0 39.5 + - - +
91L LEU* 3.5 6.7 - - - +
93L ASP* 1.3 73.0 - - - +
95L ILE* 1.3 66.1 + - - +
97L ARG* 3.2 24.0 + - + +
98L ASP* 3.1 27.0 + - - +
207L LEU* 3.3 41.7 - - + +
210L GLU* 3.6 32.1 - - + +
211L ALA* 3.6 25.1 - - + +
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Residues in contact with ILE 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L LEU* 3.0 26.0 + - + +
92L ALA 3.7 4.0 - - - +
94L LEU* 1.3 75.2 - - - +
96L GLU* 1.3 58.4 + - - +
98L ASP 3.2 3.8 - - - +
99L ARG* 2.9 25.0 + - + -
102L LEU* 4.0 17.2 - - + +
122L LEU* 4.9 11.4 - - + -
125L VAL* 4.1 18.6 - - + -
126L LEU* 3.9 16.6 - - + -
129L LEU* 3.8 28.3 - - + -
172L LEU* 6.3 1.3 - - + -
204L VAL* 4.1 21.5 - - + -
207L LEU* 3.6 22.0 - - + -
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Residues in contact with GLU 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J ARG* 5.1 1.0 + - - -
92L ALA 2.9 15.2 + - - +
93L ASP* 3.7 5.2 - - - +
94L LEU 3.2 0.2 - - - -
95L ILE* 1.3 74.2 - - - +
97L ARG* 1.3 66.6 + - - +
99L ARG* 3.3 32.3 + - - +
126L LEU* 3.8 21.7 - - + +
130L ARG* 2.9 35.1 + - - +
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Residues in contact with ARG 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L ARG* 5.6 0.4 - - - +
93L ASP 3.0 13.8 + - - +
94L LEU* 3.2 22.3 + - + +
96L GLU* 1.3 77.9 - - - +
98L ASP* 1.3 90.2 + - - +
99L ARG 3.3 2.1 + - - -
100L THR* 5.1 1.2 + - - -
203L TYR* 4.6 2.2 + - - -
207L LEU* 3.5 9.3 - - - +
210L GLU* 2.9 41.2 + - - -
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Residues in contact with ASP 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L LEU 3.1 8.2 + - - +
95L ILE 3.2 5.6 - - - +
96L GLU 3.2 0.2 - - - -
97L ARG* 1.3 118.0 + - - +
99L ARG* 1.3 55.7 + - - +
100L THR 3.5 2.2 - - - -
101L TYR* 3.4 11.6 + - + -
102L LEU* 2.9 32.9 + - + +
203L TYR* 2.9 42.7 + - + -
207L LEU* 3.5 6.3 - - + +
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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