Contacts of the helix formed by residues 80 - 98 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ARG 3.5 2.3 + - - +
79J MET* 1.3 78.0 - - - +
81J ALA* 1.3 60.6 + - - +
82J SER* 4.0 6.1 - - - +
83J HIS* 2.9 25.6 + - + +
84J ARG* 3.2 9.5 + - - +
147K ASP* 3.6 28.7 - - - +
148K GLY* 3.0 18.0 + - - -
498K LYS* 2.7 33.7 + - - +
127L LYS* 5.4 2.9 + - - -
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Residues in contact with ALA 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J MET 3.6 2.2 + - - -
80J ASP* 1.3 70.7 - - - +
82J SER* 1.3 63.6 + - - +
84J ARG* 3.0 34.6 + - - +
85J GLY 3.2 7.4 + - - -
136J ALA* 3.3 32.1 - - - +
137J ASP* 3.9 14.1 - - + -
145K PRO* 4.1 23.1 + - + +
147K ASP* 5.0 0.2 + - - -
498K LYS* 4.8 4.0 - - - +
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Residues in contact with SER 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ASP* 4.0 3.5 - - - +
81J ALA* 1.3 79.4 - - - +
83J HIS* 1.3 60.7 + - - +
85J GLY* 3.2 4.0 + - - +
86J ARG* 3.0 31.0 + - - +
136J ALA* 5.2 0.2 - - - -
137J ASP* 3.6 28.5 - - - +
145K PRO 5.3 0.4 + - - -
147K ASP* 2.8 32.2 + - - -
127L LYS* 5.5 5.2 - - - +
462L GLN* 4.5 3.1 - - - -
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Residues in contact with HIS 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J MET* 3.5 38.7 - - + +
80J ASP* 2.9 21.3 + - + +
82J SER* 1.3 78.7 + - - +
84J ARG* 1.3 64.9 + - - +
85J GLY 3.0 1.8 - - - -
86J ARG* 3.1 18.9 + - + +
87J LEU* 3.0 36.5 + - + +
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Residues in contact with ARG 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J TRP* 3.5 37.2 + - + -
79J MET* 4.2 20.6 + - + -
80J ASP 3.2 7.0 + - - +
81J ALA* 3.0 27.4 + - - +
83J HIS* 1.3 75.6 - - - +
85J GLY* 1.3 62.4 + - - +
87J LEU* 3.3 7.1 + - - +
88J LEU* 3.1 27.2 + - - +
136J ALA* 3.4 21.3 + - + -
183J LEU 3.4 17.9 - - - +
184J ALA* 3.0 25.4 + - - -
185J THR* 3.9 8.5 + - - +
186J GLY* 3.3 16.2 - - - +
213J PHE* 5.0 1.0 - - - -
500K SER* 4.1 22.6 - - - -
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Residues in contact with GLY 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J ALA 3.2 4.8 + - - -
82J SER* 3.2 8.5 + - - -
83J HIS 3.0 0.6 - - - -
84J ARG* 1.3 77.9 - - - +
86J ARG* 1.3 59.2 + - - +
88J LEU* 3.2 1.6 + - - -
89J ASN* 2.9 28.8 + - - -
133J ALA* 3.4 37.8 - - - +
136J ALA* 3.7 6.8 - - - +
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Residues in contact with ARG 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J SER* 3.0 21.0 + - - +
83J HIS* 3.1 27.5 + - + +
85J GLY* 1.3 75.2 - - - +
87J LEU* 1.3 58.1 + - + +
89J ASN* 3.2 31.3 + - - +
90J ARG* 2.9 28.5 + - - +
89L ASN* 5.1 3.4 + - - -
93L ASP* 4.9 3.0 + - - -
96L GLU* 5.1 0.8 + - - -
130L ARG* 3.7 55.7 - - - +
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Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J TRP* 4.0 5.2 - - + -
79J MET* 3.8 33.7 - - + -
83J HIS* 3.0 27.3 + - + +
84J ARG 3.7 6.5 - - - +
85J GLY 3.3 0.2 - - - -
86J ARG* 1.3 76.4 - - - +
88J LEU* 1.3 56.7 + - - +
90J ARG* 3.3 5.7 + - + +
91J LEU 2.9 23.4 + - - -
211J ALA* 3.3 28.1 - - - +
212J GLY* 3.8 14.6 - - - +
213J PHE* 3.6 49.9 - - + +
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Residues in contact with LEU 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ARG 3.1 17.8 + - - +
85J GLY* 3.2 8.3 + - - +
87J LEU* 1.3 75.7 - - - +
89J ASN* 1.3 57.7 + - - +
91J LEU* 3.3 8.7 + - + +
92J ALA* 3.0 27.0 + - - +
129J LEU* 4.1 31.7 - - + +
132J TYR* 3.9 9.4 - - + +
133J ALA* 3.6 33.9 - - + +
179J LEU 4.8 1.6 - - - +
180J GLY 4.1 8.1 - - - +
183J LEU* 4.2 20.2 - - + -
184J ALA* 4.1 22.4 - - - +
213J PHE* 4.1 17.3 - - + -
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Residues in contact with ASN 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J GLY 2.9 17.9 + - - +
86J ARG* 3.2 32.1 + - - +
88J LEU* 1.3 76.2 - - - +
90J ARG* 1.3 62.0 + - - +
92J ALA* 3.4 6.0 + - - +
93J ASP* 3.1 30.7 + - - +
130J ARG* 3.7 24.3 + - - +
133J ALA* 3.6 21.0 - - - +
134J GLY 5.3 0.2 - - - +
86L ARG* 5.1 2.5 + - - -
89L ASN* 5.0 17.6 + - - +
130L ARG* 6.4 0.2 - - - +
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Residues in contact with ARG 90 (chain J).
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 2.9 12.8 + - - +
87J LEU* 3.5 13.2 - - + +
88J LEU 3.2 0.2 - - - -
89J ASN* 1.3 75.2 - - - +
91J LEU* 1.3 65.9 + - - +
93J ASP* 3.1 21.5 + - - +
94J LEU* 2.9 49.1 + - + +
97J ARG* 5.6 0.6 - - - +
210J GLU* 4.6 10.5 + - - +
211J ALA* 3.7 30.6 + - - +
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Residues in contact with LEU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J LEU 2.9 14.0 + - - +
88J LEU* 3.6 11.2 - - + +
90J ARG* 1.3 74.7 - - - +
92J ALA* 1.3 63.3 + - - +
94J LEU* 3.2 4.7 + - - +
95J ILE* 3.0 41.6 + - + +
129J LEU* 3.9 25.4 - - + -
179J LEU* 5.0 6.7 - - + -
183J LEU* 5.6 1.8 - - + -
204J VAL* 4.3 5.2 - - + +
207J LEU* 3.8 16.6 - - + +
208J ILE* 3.8 49.1 - - + +
211J ALA* 4.0 5.8 - - - +
213J PHE* 4.2 15.7 - - + -
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Residues in contact with ALA 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J LEU 3.0 14.3 + - - +
89J ASN 3.5 10.1 - - - +
91J LEU* 1.3 77.0 - - - +
93J ASP* 1.3 56.0 + - - +
95J ILE* 3.2 1.5 + - - -
96J GLU* 2.9 25.1 + - - +
126J LEU* 3.1 19.9 - - + +
129J LEU* 4.2 19.0 - - + +
130J ARG* 3.7 36.1 - - + +
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Residues in contact with ASP 93 (chain J).
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* 3.1 19.3 + - - +
90J ARG* 3.1 26.5 + - - +
92J ALA* 1.3 75.0 - - - +
94J LEU* 1.3 58.6 + - - +
96J GLU* 3.3 3.7 + - - +
97J ARG* 3.0 27.5 + - - +
130J ARG* 3.0 24.2 + - - +
86L ARG* 4.8 4.3 + - - -
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ARG* 2.9 38.9 + - + +
91J LEU* 3.6 6.7 - - - +
93J ASP* 1.3 75.8 - - - +
95J ILE* 1.3 63.2 + - - +
97J ARG* 3.2 36.4 + - - +
98J ASP* 3.1 25.6 + - - +
207J LEU* 3.2 43.5 - - + +
210J GLU* 3.5 21.3 - - + +
211J ALA* 3.5 23.8 - - + +
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Residues in contact with ILE 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU* 3.0 22.9 + - + +
92J ALA 3.2 7.2 + - - +
94J LEU* 1.3 74.0 - - - +
96J GLU* 1.3 60.3 + - - +
98J ASP 3.3 2.9 + - - -
99J ARG* 2.9 25.5 + - - -
102J LEU* 3.8 17.7 - - + +
122J LEU* 4.4 11.9 - - + -
125J VAL* 4.2 17.9 - - + -
126J LEU* 3.7 15.9 - - + -
129J LEU* 3.7 29.6 - - + -
172J LEU* 6.0 1.1 - - + -
204J VAL* 4.2 21.1 - - + -
207J LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ALA 2.9 16.3 + - - +
93J ASP* 3.7 5.3 - - - +
94J LEU 3.3 0.2 - - - -
95J ILE* 1.3 74.3 - - - +
97J ARG* 1.3 65.6 + - - +
99J ARG* 3.2 34.7 + - - +
126J LEU* 3.7 22.8 - - + +
130J ARG* 2.8 31.0 + - - +
86L ARG* 5.1 1.4 + - - -
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Residues in contact with ARG 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ARG* 5.6 0.6 - - - +
93J ASP 3.0 13.2 + - - +
94J LEU* 3.2 24.8 - - - +
96J GLU* 1.3 78.7 - - - +
98J ASP* 1.3 89.4 + - - +
99J ARG 3.6 1.4 + - - -
100J THR 5.2 0.9 + - - -
203J TYR* 4.3 2.8 + - - -
207J LEU* 3.8 8.1 - - - +
210J GLU* 2.8 42.6 + - - -
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Residues in contact with ASP 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J LEU 3.1 9.0 + - - +
95J ILE 3.3 4.9 - - - +
96J GLU 3.2 0.2 - - - -
97J ARG* 1.3 118.9 + - - +
99J ARG* 1.3 51.4 + - - -
100J THR 3.4 2.7 - - - -
101J TYR* 3.3 13.0 + - + -
102J LEU* 2.8 39.3 + - + +
203J TYR* 2.7 42.4 + - + -
207J LEU* 3.6 5.0 - - - +
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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
------------------------------------------------------------
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