Contacts of the helix formed by residues 80 - 98 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E LYS* 5.5 2.8 + - - -
147F ASP* 3.4 33.6 - - - +
148F GLY* 2.9 17.0 + - - -
498F LYS* 2.9 27.1 + - - +
78G ARG 3.5 3.3 + - - +
79G MET* 1.3 78.2 - - - +
81G ALA* 1.3 64.6 + - - +
82G SER* 3.9 6.5 + - - +
83G HIS* 2.9 20.2 + - + +
84G ARG* 3.3 9.0 + - - +
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F PRO* 4.2 21.9 + - + +
147F ASP* 4.9 0.8 + - - -
498F LYS* 4.9 3.6 - - - +
79G MET 3.5 2.4 + - - -
80G ASP* 1.3 71.4 - - - +
82G SER* 1.3 63.6 + - - +
84G ARG* 2.9 35.6 + - - +
85G GLY 3.2 7.3 + - - -
136G ALA* 3.3 32.4 - - - +
137G ASP* 3.9 13.5 - - + -
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Residues in contact with SER 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E LYS* 5.3 7.1 - - - +
462E GLN* 4.7 2.0 - - - -
145F PRO 5.3 0.2 + - - -
147F ASP* 2.6 34.6 + - - -
80G ASP* 3.9 3.0 + - - +
81G ALA* 1.3 79.0 - - - +
83G HIS* 1.3 60.5 + - - +
85G GLY* 3.2 4.5 + - - +
86G ARG* 3.0 30.0 + - - +
136G ALA* 5.1 0.4 - - - -
137G ASP* 3.5 29.1 - - - +
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Residues in contact with HIS 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G MET* 3.6 36.8 - - + +
80G ASP* 2.9 19.7 + - + +
82G SER* 1.3 79.6 + - - +
84G ARG* 1.3 65.9 + - - +
85G GLY 3.0 1.1 - - - -
86G ARG* 3.1 20.1 + - + +
87G LEU* 3.0 37.3 + - + +
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Residues in contact with ARG 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F SER* 3.8 25.9 - - - -
76G TRP* 3.8 27.5 + - + -
79G MET* 4.0 19.9 + - + -
80G ASP 3.3 9.2 + - - +
81G ALA* 2.9 26.5 + - - +
83G HIS* 1.3 75.4 - - - +
85G GLY* 1.3 63.5 + - - +
87G LEU* 3.2 8.5 + - - +
88G LEU* 3.1 26.9 + - - +
136G ALA* 3.2 22.5 + - + -
183G LEU 3.4 19.3 - - - +
184G ALA* 2.9 26.6 + - - -
185G THR* 4.0 7.7 + - - +
186G GLY* 3.4 17.2 - - - +
213G PHE* 5.0 0.9 - - - -
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Residues in contact with GLY 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ALA 3.2 4.2 + - - -
82G SER* 3.2 8.7 + - - -
83G HIS 3.0 0.6 - - - -
84G ARG* 1.3 80.0 - - - +
86G ARG* 1.3 60.7 + - - +
88G LEU 3.3 1.4 + - - -
89G ASN* 2.9 24.8 + - - -
133G ALA* 3.3 37.8 - - - +
136G ALA* 3.7 5.7 - - - +
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Residues in contact with ARG 86 (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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89E ASN* 5.1 3.2 + - - -
93E ASP* 4.6 4.2 + - - -
96E GLU* 4.7 2.2 + - - -
130E ARG* 3.4 60.7 - - - +
82G SER* 3.0 22.2 + - - +
83G HIS* 3.4 28.9 - - + +
85G GLY* 1.3 76.1 - - - +
87G LEU* 1.3 58.5 + - + +
89G ASN* 3.3 27.3 + - - +
90G ARG* 2.9 28.3 + - - +
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G TRP* 4.0 12.6 - - + -
79G MET* 3.4 41.3 - - + -
83G HIS* 3.0 26.2 + - + +
84G ARG* 3.5 7.0 - - - +
85G GLY 3.2 0.2 - - - -
86G ARG* 1.3 75.8 - - - +
88G LEU* 1.3 59.2 + - - +
90G ARG* 3.1 6.6 + - + +
91G LEU* 2.9 28.8 + - - +
211G ALA* 3.5 26.0 - - - +
212G GLY* 4.1 19.1 - - - +
213G PHE* 3.5 26.6 - - + +
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Residues in contact with LEU 88 (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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84G ARG 3.1 17.2 + - - +
85G GLY* 3.8 1.3 - - - +
87G LEU* 1.3 74.5 - - - +
89G ASN* 1.3 58.5 + - - +
91G LEU* 3.3 9.1 + - + +
92G ALA* 3.0 28.2 + - - +
129G LEU* 4.2 33.6 - - + +
132G TYR* 4.2 1.3 - - + -
133G ALA* 3.7 33.9 - - + +
179G LEU 4.7 0.2 - - - +
180G GLY* 3.9 13.5 - - - +
183G LEU* 4.2 22.4 - - + -
184G ALA* 3.8 32.8 - - + +
213G PHE* 4.2 14.1 - - + -
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Residues in contact with ASN 89 (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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86E ARG* 4.7 6.4 + - - -
89E ASN* 4.9 15.4 + - - +
130E ARG* 6.3 0.4 - - - +
85G GLY 2.9 21.7 + - - +
86G ARG* 3.6 27.6 - - - +
87G LEU 3.2 0.2 - - - -
88G LEU* 1.3 77.4 - - - +
90G ARG* 1.3 61.2 + - - +
92G ALA* 3.3 5.7 + - - +
93G ASP* 3.0 31.5 + - - +
130G ARG* 3.7 24.3 + - - +
133G ALA* 3.5 20.2 - - - +
134G GLY* 6.0 0.6 - - - -
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Residues in contact with ARG 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ARG 2.9 14.1 + - - +
87G LEU* 3.5 11.9 - - + +
89G ASN* 1.3 73.4 - - - +
91G LEU* 1.3 66.6 + - - +
93G ASP* 3.1 22.6 + - - +
94G LEU* 3.0 54.6 + - - +
97G ARG* 5.2 1.0 - - - +
210G GLU* 4.5 12.3 + - - +
211G ALA* 3.8 28.9 + - + +
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Residues in contact with LEU 91 (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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87G LEU 2.9 15.9 + - - +
88G LEU* 3.6 12.8 - - + +
90G ARG* 1.3 78.2 - - - +
92G ALA* 1.3 63.4 + - - +
94G LEU* 3.2 3.3 + - - +
95G ILE* 3.0 28.8 + - + +
129G LEU* 4.1 26.7 - - + -
179G LEU* 5.1 7.0 - - + -
183G LEU* 5.5 1.8 - - + -
204G VAL* 4.4 6.5 - - + +
207G LEU* 3.8 30.3 - - + +
208G ILE* 3.9 35.4 - - + +
211G ALA* 4.0 5.4 - - + +
213G PHE* 4.2 14.6 - - + -
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU 3.0 14.2 + - - +
89G ASN 3.6 8.5 - - - +
91G LEU* 1.3 78.1 - - - +
93G ASP* 1.3 56.3 + - - +
95G ILE* 3.2 1.5 + - - -
96G GLU* 2.9 24.6 + - - +
126G LEU* 3.2 21.1 - - + +
129G LEU* 4.2 19.0 - - + +
130G ARG* 3.7 36.6 - - + +
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Residues in contact with ASP 93 (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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86E ARG* 5.3 2.9 + - - -
93E ASP* 5.4 3.3 - - - +
89G ASN* 3.0 22.9 + - - +
90G ARG* 3.1 25.8 + - - +
92G ALA* 1.3 77.6 - - - +
94G LEU* 1.3 57.2 + - - +
96G GLU* 3.2 4.8 + - - +
97G ARG* 2.9 27.9 + - - +
130G ARG* 3.1 24.2 + - - +
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Residues in contact with LEU 94 (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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90G ARG* 3.0 48.4 + - - +
91G LEU* 3.2 6.5 + - - +
93G ASP* 1.3 71.7 - - - +
95G ILE* 1.3 67.0 + - - +
97G ARG* 3.2 34.5 + - + +
98G ASP* 3.1 26.2 + - - +
207G LEU* 3.5 42.8 - - + +
210G GLU* 3.7 14.8 - - + +
211G ALA* 3.6 25.4 - - + +
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Residues in contact with ILE 95 (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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91G LEU* 3.0 23.9 + - + +
92G ALA 3.7 6.5 - - - +
94G LEU* 1.3 75.8 - - - +
96G GLU* 1.3 58.0 + - - +
98G ASP 3.2 3.8 + - - -
99G ARG* 2.9 26.0 + - - +
102G LEU* 3.9 10.3 - - + -
122G LEU* 3.6 27.6 - - + -
125G VAL* 4.0 15.0 - - + -
126G LEU* 3.8 12.1 - - + -
129G LEU* 3.6 30.7 - - + -
172G LEU* 6.0 1.1 - - + -
204G VAL* 4.3 19.7 - - + -
207G LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 96 (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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86E ARG* 5.2 0.7 + - - -
92G ALA 2.9 14.6 + - - +
93G ASP* 3.2 7.8 + - - +
95G ILE* 1.3 73.4 - - - +
97G ARG* 1.3 64.9 + - - +
99G ARG* 3.2 35.1 + - - +
126G LEU* 3.7 20.7 - - + +
130G ARG* 2.8 32.5 + - - +
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Residues in contact with ARG 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G ARG* 5.2 1.2 - - - +
93G ASP 2.9 13.8 + - - +
94G LEU* 3.2 24.1 + - + +
96G GLU* 1.3 79.4 - - - +
98G ASP* 1.3 89.5 + - - +
99G ARG 3.6 1.6 + - - -
100G THR 5.2 0.9 + - - -
203G TYR* 4.6 1.6 + - - -
207G LEU* 3.8 8.3 - - - +
210G GLU* 2.8 42.4 + - - -
3125G EDO 5.8 0.6 + - - -
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Residues in contact with ASP 98 (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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94G LEU 3.1 10.3 + - - +
95G ILE 3.3 4.7 - - - +
96G GLU 3.2 0.2 - - - -
97G ARG* 1.3 116.7 + - - +
99G ARG* 1.3 57.3 + - - +
100G THR 3.5 2.5 - - - -
101G TYR* 3.3 6.5 + - + +
102G LEU* 2.9 32.7 + - + +
203G TYR* 2.8 40.9 + - + -
207G LEU* 3.7 4.8 - - + +
3125G EDO 4.3 18.4 + - - -
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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) + - + + + + + -
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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