Contacts of the helix formed by residues 80 - 98 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I ARG 3.5 2.8 + - - +
79I MET* 1.3 78.3 - - - +
81I ALA* 1.3 65.3 + - - +
82I SER* 4.0 6.3 - - - +
83I HIS* 2.9 20.8 + - + +
84I ARG* 3.2 9.9 + - - +
127K LYS* 5.5 1.7 + - - -
147L ASP* 3.1 37.6 - - - +
148L GLY* 3.0 17.3 + - - -
498L LYS* 2.8 30.0 + - - +
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Residues in contact with ALA 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I MET 3.6 1.8 + - - -
80I ASP* 1.3 72.2 - - - +
82I SER* 1.3 62.5 + - - +
84I ARG* 3.1 34.6 + - - +
136I ALA* 3.2 42.0 - - - +
137I ASP* 3.9 13.5 - - + -
145L PRO* 4.0 25.6 + - + +
498L LYS* 4.9 2.8 - - - +
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Residues in contact with SER 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ASP* 3.1 3.5 - - - +
81I ALA* 1.3 78.0 - - - +
83I HIS* 1.3 60.8 + - - +
85I GLY* 3.2 5.1 + - - +
86I ARG* 3.1 29.9 + - - +
137I ASP* 3.6 28.0 - - - +
127K LYS* 5.3 5.6 - - - +
462K GLN* 4.5 2.9 - - - -
145L PRO 5.1 0.2 + - - -
147L ASP* 2.8 33.5 + - - -
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Residues in contact with HIS 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I MET* 3.3 38.7 - - + +
80I ASP* 2.9 18.3 + - + +
82I SER* 1.3 78.0 + - - +
84I ARG* 1.3 66.0 + - - +
85I GLY 3.0 1.8 - - - -
86I ARG* 3.1 18.5 + - + +
87I LEU* 3.0 41.0 + - + +
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Residues in contact with ARG 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I TRP* 3.7 30.9 + - + -
79I MET* 4.0 18.1 + - + -
80I ASP 3.2 8.1 + - - +
81I ALA* 3.1 28.8 + - - +
83I HIS* 1.3 75.0 - - - +
85I GLY* 1.3 62.4 + - - +
87I LEU* 3.3 6.3 + - - +
88I LEU* 3.1 27.1 + - - +
136I ALA* 3.2 23.5 + - + -
183I LEU 3.5 18.4 - - - +
184I ALA* 2.9 26.2 + - - -
185I THR* 3.9 8.0 + - - +
186I GLY* 3.4 18.6 - - - +
213I PHE* 5.0 1.4 - - - -
500L SER* 3.7 26.9 - - - -
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Residues in contact with GLY 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I ALA 3.3 4.2 + - - -
82I SER* 3.2 8.6 + - - -
83I HIS 3.0 0.6 - - - -
84I ARG* 1.3 77.9 - - - +
86I ARG* 1.3 63.7 + - - +
88I LEU* 3.4 0.7 + - - -
89I ASN* 3.0 25.0 + - - -
133I ALA* 3.4 37.7 - - - +
136I ALA* 3.6 6.2 - - - +
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Residues in contact with ARG 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I SER* 3.1 16.7 + - - +
83I HIS* 3.1 25.9 + - + +
85I GLY* 1.3 77.6 - - - +
87I LEU* 1.3 58.2 + - - +
89I ASN* 3.3 30.4 + - - +
90I ARG* 2.9 29.6 + - - +
89K ASN* 4.5 5.1 + - - -
93K ASP* 4.7 4.0 + - - -
96K GLU* 5.0 0.8 + - - -
130K ARG* 3.4 62.2 - - - +
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I TRP* 4.0 3.8 - - + -
79I MET* 3.7 34.3 - - + -
83I HIS* 3.0 30.0 + - + +
84I ARG 3.6 6.5 - - - +
86I ARG* 1.3 77.8 - - - +
88I LEU* 1.3 55.7 + - - +
90I ARG* 3.2 5.8 + - + +
91I LEU 2.9 24.4 + - - -
211I ALA* 3.4 26.1 - - - +
212I GLY* 4.1 12.1 - - - +
213I PHE* 3.6 49.2 - - + +
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Residues in contact with LEU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ARG 3.1 18.8 + - - +
85I GLY* 3.8 0.4 - - - +
87I LEU* 1.3 76.3 - - - +
89I ASN* 1.3 58.5 + - - +
91I LEU* 3.3 8.9 + - + +
92I ALA* 3.0 27.2 + - - +
129I LEU* 4.1 32.3 - - + +
132I TYR* 3.9 8.7 - - + +
133I ALA* 3.7 34.8 - - + +
136I ALA* 5.4 0.2 - - + -
179I LEU* 4.7 3.4 - - + +
180I GLY* 4.0 5.4 - - - +
183I LEU* 4.1 29.6 - - + -
184I ALA* 3.9 26.7 - - + +
213I PHE* 4.1 9.4 - - + -
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Residues in contact with ASN 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I GLY 3.0 20.8 + - - +
86I ARG* 3.7 29.2 - - - +
88I LEU* 1.3 77.0 - - - +
90I ARG* 1.3 56.9 + - - +
92I ALA* 3.4 5.5 + - - +
93I ASP* 3.0 35.1 + - - +
130I ARG* 3.6 27.4 + - - +
133I ALA* 3.5 19.8 - - - +
134I GLY* 5.3 0.4 - - - +
86K ARG* 4.9 5.2 + - - -
89K ASN* 4.6 15.9 + - - +
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Residues in contact with ARG 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ARG 2.9 13.2 + - - +
87I LEU* 3.2 13.4 + - + +
89I ASN* 1.3 73.9 - - - +
91I LEU* 1.3 65.1 + - - +
93I ASP* 3.1 19.0 + - - +
94I LEU* 3.0 53.0 + - + +
97I ARG* 5.2 0.8 - - - +
210I GLU* 4.4 14.3 + - - +
211I ALA* 3.8 28.8 + - + +
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Residues in contact with LEU 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I LEU 2.9 13.5 + - - +
88I LEU* 3.6 12.3 - - + +
90I ARG* 1.3 75.5 - - - +
92I ALA* 1.3 64.9 + - - +
94I LEU* 3.1 5.7 + - - +
95I ILE* 2.9 40.6 + - + +
129I LEU* 4.0 22.4 - - + -
179I LEU* 5.2 7.0 - - + -
183I LEU* 5.5 1.6 - - + -
204I VAL* 4.2 6.1 - - + +
207I LEU* 3.8 16.4 - - + +
208I ILE* 3.7 48.7 - - + +
211I ALA* 4.1 5.6 - - + -
213I PHE* 4.2 16.6 - - + -
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Residues in contact with ALA 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I LEU 3.0 13.0 + - - +
89I ASN 3.5 9.4 - - - +
90I ARG 3.2 0.2 - - - -
91I LEU* 1.3 77.5 - - - +
93I ASP* 1.3 57.0 + - - +
95I ILE* 3.1 2.2 + - - -
96I GLU* 2.9 26.2 + - - +
126I LEU* 3.3 18.7 - - + +
129I LEU* 4.2 18.1 - - + +
130I ARG* 3.7 36.8 - - + +
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Residues in contact with ASP 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I ASN* 3.0 20.9 + - - +
90I ARG* 3.1 27.0 + - - +
92I ALA* 1.3 76.0 - - - +
94I LEU* 1.3 57.9 + - - +
96I GLU* 3.3 6.0 + - - +
97I ARG* 3.0 26.0 + - - +
130I ARG* 3.1 24.2 + - - +
86K ARG* 4.7 4.5 + - - -
93K ASP* 5.7 1.0 - - - +
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ARG* 3.0 49.3 + - - +
91I LEU* 3.6 6.5 - - - +
93I ASP* 1.3 73.7 - - - +
95I ILE* 1.3 65.0 + - - +
97I ARG* 3.1 31.4 + - - +
98I ASP* 3.0 26.3 + - - +
207I LEU* 3.5 41.7 - - + +
210I GLU* 3.8 18.2 - - + +
211I ALA* 3.7 22.9 - - + +
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Residues in contact with ILE 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LEU* 2.9 25.8 + - + +
92I ALA 3.5 7.0 - - - +
94I LEU* 1.3 75.6 - - - +
96I GLU* 1.3 62.2 + - - +
98I ASP 3.3 4.0 + - - -
99I ARG* 3.0 21.0 + - - -
102I LEU* 4.1 8.2 - - + +
122I LEU* 3.8 23.6 - - + -
125I VAL* 4.0 14.1 - - + -
126I LEU* 3.6 15.9 - - + -
129I LEU* 3.5 32.8 - - + -
172I LEU* 6.3 0.9 - - + -
204I VAL* 4.3 20.0 - - + -
207I LEU* 3.9 19.5 - - + -
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I ALA 2.9 13.1 + - - +
93I ASP* 3.6 10.7 - - - +
94I LEU 3.2 0.2 - - - -
95I ILE* 1.3 75.4 - - - +
97I ARG* 1.3 64.9 + - - +
99I ARG* 3.2 34.0 + - - +
126I LEU* 3.8 22.7 - - + +
130I ARG* 2.9 34.3 + - - +
86K ARG* 4.8 2.6 + - - -
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ARG* 5.2 1.0 - - - +
93I ASP 3.0 13.4 + - - +
94I LEU* 3.1 25.4 + - + +
96I GLU* 1.3 79.0 - - - +
98I ASP* 1.3 88.9 + - - +
99I ARG 3.3 2.0 + - - -
100I THR 5.1 0.9 + - - -
203I TYR* 4.4 2.2 + - - -
207I LEU* 3.6 7.9 - - - +
210I GLU* 2.9 41.4 + - - -
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Residues in contact with ASP 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I LEU 3.0 9.6 + - - +
95I ILE 3.3 5.2 - - - +
96I GLU 3.2 0.2 - - - -
97I ARG* 1.3 115.7 + - - +
99I ARG* 1.3 56.2 - - - +
100I THR 3.4 2.2 - - - -
101I TYR* 3.4 7.1 + - + -
102I LEU* 2.9 33.9 + - + +
203I TYR* 2.6 41.5 + - + -
207I LEU* 3.6 3.7 - - + +
3127I EDO 4.2 19.6 + - - -
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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