Contacts of the helix formed by residues 80 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ASP* 3.4 34.2 - - - +
148A GLY* 2.8 16.6 + - - -
498A LYS* 2.8 31.9 + - - +
127B LYS* 5.4 2.3 + - - -
78D ARG 3.6 3.1 + - - +
79D MET* 1.3 78.2 - - - +
81D ALA* 1.3 60.5 - - - +
82D SER* 3.8 6.3 - - - +
83D HIS* 2.9 24.7 + - + +
84D ARG* 3.2 10.2 + - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 4.1 22.0 + - + +
146A ILE 5.8 0.2 + - - -
147A ASP* 4.9 0.2 + - - -
498A LYS* 5.0 3.2 - - - +
79D MET 3.5 2.0 + - - -
80D ASP* 1.3 71.3 - - - +
82D SER* 1.3 63.2 + - - +
84D ARG* 3.0 36.7 + - - +
85D GLY 3.3 6.9 + - - -
136D ALA* 3.3 31.7 - - - +
137D ASP* 3.9 14.8 - - + -
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Residues in contact with SER 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO 5.3 0.6 + - - -
147A ASP* 2.6 34.3 + - - -
127B LYS* 5.3 6.0 - - - -
462B GLN* 4.5 3.4 - - - -
80D ASP* 3.8 3.7 - - - +
81D ALA* 1.3 77.4 - - - +
83D HIS* 1.3 59.3 + - - +
85D GLY* 3.2 4.7 + - - +
86D ARG* 3.1 30.0 + - - +
136D ALA* 5.0 0.9 - - - -
137D ASP* 3.4 27.8 - - - +
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D MET* 3.5 38.1 - - + +
80D ASP* 2.9 19.1 + - + +
82D SER* 1.3 78.9 + - - +
84D ARG* 1.3 64.2 + - - +
85D GLY 3.0 1.3 - - - -
86D ARG* 3.0 23.3 + - + +
87D LEU* 3.0 38.1 + - + +
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A SER* 3.7 26.5 - - - +
76D TRP* 3.8 30.6 + - + -
79D MET* 4.0 20.7 + - + -
80D ASP 3.2 9.0 + - - +
81D ALA* 3.0 26.5 + - - +
83D HIS* 1.3 75.6 - - - +
85D GLY* 1.3 62.2 - - - +
87D LEU* 3.3 8.4 + - - +
88D LEU* 3.1 28.4 + - - +
136D ALA* 3.4 21.7 + - + -
183D LEU 3.6 18.6 - - - +
184D ALA* 2.9 26.0 + - - -
185D THR* 3.7 10.2 + - - +
186D GLY* 3.4 20.0 - - - +
213D PHE* 5.0 0.9 - - - -
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Residues in contact with GLY 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ALA 3.3 4.4 + - - -
82D SER 3.2 9.0 + - - -
83D HIS 3.0 0.8 - - - -
84D ARG* 1.3 77.4 - - - +
86D ARG* 1.3 63.5 + - - +
88D LEU* 3.3 1.8 + - - -
89D ASN* 3.0 25.9 + - - -
133D ALA* 3.4 36.6 - - - +
136D ALA* 3.6 7.0 - - - +
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Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASN* 5.0 2.6 + - - -
93B ASP* 4.6 4.4 + - - -
96B GLU* 4.8 1.4 + - - -
130B ARG* 3.5 59.5 - - - +
82D SER* 3.1 21.0 + - - +
83D HIS* 3.0 30.4 + - + +
85D GLY* 1.3 75.3 - - - +
87D LEU* 1.3 59.2 + - + +
89D ASN* 3.2 31.6 + - - +
90D ARG* 2.9 29.4 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 4.0 15.5 - - + -
79D MET* 3.7 34.5 - - + -
83D HIS* 3.0 28.7 + - + +
84D ARG* 3.6 6.3 - - - +
85D GLY 3.2 0.2 - - - -
86D ARG* 1.3 78.1 - - + +
88D LEU* 1.3 56.1 + - - +
90D ARG* 3.2 7.2 + - + +
91D LEU* 2.9 28.8 + - - +
211D ALA* 3.6 23.0 - - - +
212D GLY* 4.2 13.0 - - - +
213D PHE* 3.5 35.5 - - + -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ARG 3.1 18.5 + - - +
85D GLY* 3.3 1.8 + - - +
87D LEU* 1.3 74.4 - - - +
89D ASN* 1.3 57.6 + - - +
91D LEU* 3.3 8.1 + - + +
92D ALA* 3.0 27.7 + - - +
129D LEU* 4.1 32.0 - - + +
132D TYR* 4.1 1.3 - - + -
133D ALA* 3.6 35.4 - - + +
179D LEU 4.7 1.3 - - - +
180D GLY* 4.0 7.9 - - - +
183D LEU* 4.1 24.5 - - + -
184D ALA* 3.8 35.2 - - + +
213D PHE* 4.1 13.7 - - + -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 4.9 3.1 + - - -
89B ASN* 4.4 23.0 + - - +
130B ARG* 6.2 1.0 - - - +
85D GLY 3.0 19.3 + - - -
86D ARG* 3.5 29.9 - - - +
88D LEU* 1.3 73.0 - - - +
90D ARG* 1.3 60.6 + - - +
92D ALA* 3.4 6.6 + - - +
93D ASP* 3.0 35.1 + - - +
130D ARG* 3.7 21.0 + - - +
133D ALA* 3.5 19.2 - - - +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG* 2.9 14.3 + - - +
87D LEU* 3.5 11.9 - - + +
89D ASN* 1.3 74.7 - - - +
91D LEU* 1.3 64.4 + - - +
93D ASP* 3.1 20.4 + - - +
94D LEU* 3.0 50.7 + - + +
97D ARG* 5.6 0.2 - - - +
210D GLU* 4.6 11.9 + - - +
211D ALA* 3.7 31.0 + - + +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LEU 2.9 13.8 + - - +
88D LEU* 3.5 13.0 - - + +
90D ARG* 1.3 75.9 - - - +
92D ALA* 1.3 63.5 + - - +
94D LEU* 3.2 3.6 + - - +
95D ILE* 3.0 30.3 + - + +
129D LEU* 3.9 27.4 - - + -
179D LEU* 5.1 6.7 - - + -
183D LEU* 5.5 2.2 - - + -
204D VAL* 4.4 5.6 - - + +
207D LEU* 3.8 37.7 - - + +
208D ILE* 3.8 26.5 - - + +
211D ALA* 4.1 5.4 - - + -
213D PHE* 4.1 17.7 - - + -
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU 3.0 13.5 + - - +
89D ASN 3.4 9.0 - - - +
90D ARG 3.2 0.2 - - - -
91D LEU* 1.3 76.5 - - - +
93D ASP* 1.3 55.4 + - - +
95D ILE* 3.2 2.1 + - - -
96D GLU* 2.9 24.6 + - - +
126D LEU* 3.1 18.1 - - + +
129D LEU* 4.2 19.9 - - + +
130D ARG* 3.5 37.7 - - + +
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Residues in contact with ASP 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 4.1 7.6 + - - -
93B ASP* 5.0 7.4 - - - +
89D ASN* 3.0 21.0 + - - +
90D ARG* 3.4 25.3 + - - +
92D ALA* 1.3 75.1 - - - +
94D LEU* 1.3 57.8 + - - +
96D GLU* 3.3 4.5 + - - +
97D ARG* 3.0 26.7 + - - +
130D ARG* 3.1 25.0 + - - +
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ARG* 3.0 40.7 + - - +
91D LEU* 3.2 7.6 + - - +
93D ASP* 1.3 77.2 - - - +
95D ILE* 1.3 61.3 + - - +
97D ARG* 3.1 39.2 + - - +
98D ASP* 3.1 26.0 + - - -
207D LEU* 3.4 40.8 - - + +
210D GLU* 3.4 19.7 - - + +
211D ALA* 3.5 26.0 - - + +
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 3.0 21.7 + - + +
92D ALA 3.6 7.0 - - - +
94D LEU* 1.3 75.4 - - - +
96D GLU* 1.3 57.9 + - - +
98D ASP 3.3 4.0 + - - -
99D ARG* 3.0 24.6 + - - -
102D LEU* 4.2 10.6 - - + +
122D LEU* 3.6 27.4 - - + -
125D VAL* 4.0 15.5 - - + -
126D LEU* 3.7 13.0 - - + -
129D LEU* 3.7 31.2 - - + -
172D LEU* 6.0 0.9 - - + -
204D VAL* 4.4 20.0 - - + -
207D LEU* 3.8 21.3 - - + -
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 4.7 2.8 + - - -
92D ALA 2.9 12.7 + - - +
93D ASP* 3.6 9.0 - - - +
94D LEU 3.2 0.4 - - - -
95D ILE* 1.3 74.6 - - - +
97D ARG* 1.3 66.9 + - - +
99D ARG* 3.1 36.8 + - - +
126D LEU* 3.9 21.5 - - + -
130D ARG* 2.7 36.6 + - - +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ARG* 5.6 0.6 - - - +
93D ASP 3.0 13.0 + - - +
94D LEU* 3.2 24.6 - - - +
96D GLU* 1.3 79.9 - - - +
98D ASP* 1.3 86.8 + - - +
99D ARG 3.5 1.6 + - - -
100D THR* 5.1 0.9 + - - -
203D TYR* 4.5 2.4 + - - -
207D LEU* 3.5 9.9 - - - +
210D GLU* 2.7 41.8 + - - -
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU 3.1 9.3 + - - +
95D ILE 3.3 4.5 - - - +
96D GLU 3.2 0.2 - - - -
97D ARG* 1.3 114.8 + - - +
99D ARG* 1.3 58.0 + - - +
100D THR 3.4 2.2 - - - -
101D TYR* 3.3 13.9 + - + -
102D LEU* 2.8 33.6 + - + +
203D TYR* 2.7 43.2 + - + -
207D LEU* 3.7 4.1 - - + +
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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