Contacts of the helix formed by residues 89 - 104 (chain B) in PDB entry 1EZF
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 SER 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B MET 5.6 0.7 - - - -
87B THR 3.5 6.3 + - - -
88B ILE* 1.3 71.2 - - - +
90B VAL* 1.3 60.5 + - - +
91B GLU* 2.9 31.4 + - - -
92B LYS* 2.8 37.1 + - - +
93B LYS 2.8 10.9 + - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE 3.4 2.8 + - - +
89B SER* 1.3 71.3 - - - +
91B GLU* 1.3 67.2 + - + +
93B LYS* 4.0 9.6 - - + +
94B VAL* 3.0 34.6 + - + +
158B LEU* 4.3 26.2 - - + -
159B ASP* 4.5 20.6 - - - +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 2.9 27.2 + - - -
90B VAL* 1.3 84.8 + - + +
92B LYS* 1.3 86.1 + - + +
94B VAL* 5.2 0.7 - - - -
95B PRO* 3.2 21.0 - - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 4.3 9.6 - - + -
89B SER* 2.8 19.8 + - - +
91B GLU* 1.3 102.9 - - + +
93B LYS* 1.3 64.7 + - - +
94B VAL 3.3 1.6 - - - -
95B PRO* 3.1 13.9 - - - +
96B LEU* 3.3 22.8 + - + +
111B PHE* 6.2 1.6 - - + -
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.0 24.7 - - + +
83B GLU 2.8 23.1 + - - +
85B ASP 2.8 29.0 + - - -
86B MET* 3.6 15.8 - - - +
88B ILE* 3.6 27.4 + - + +
89B SER 2.8 15.3 + - - +
90B VAL* 4.0 8.7 - - + +
92B LYS* 1.3 76.9 - - - +
94B VAL* 1.3 64.6 + - - +
96B LEU* 3.1 9.4 + - + +
97B LEU* 2.9 39.2 + - + +
158B LEU* 3.8 27.6 - - + +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B VAL* 3.0 20.5 + - + +
91B GLU* 4.9 1.3 - - - +
93B LYS* 1.3 76.1 - - - +
95B PRO* 1.3 71.1 - - + +
97B LEU* 3.4 6.0 + - - +
98B HIS* 2.9 52.2 + - + +
155B ALA* 4.4 10.3 - - + +
158B LEU* 3.9 19.7 - - + -
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Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU 3.2 21.8 - - - +
92B LYS* 3.1 17.7 - - - +
94B VAL* 1.3 89.9 - - + +
96B LEU* 1.3 53.8 + - + +
98B HIS* 3.2 5.7 + - + +
99B ASN* 2.8 52.6 + - - +
103B PHE* 5.2 0.9 - - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 4.0 25.3 - - + +
88B ILE* 4.2 12.8 - - + -
92B LYS* 3.3 17.0 + - + +
93B LYS* 3.1 9.1 + - + +
95B PRO* 1.3 80.1 - - + +
97B LEU* 1.3 57.9 + - + +
100B PHE* 3.1 32.4 + - - +
103B PHE* 3.7 15.3 - - + -
109B TRP* 3.8 30.3 - - + +
111B PHE* 3.5 36.6 - - + -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.0 7.0 - - + -
82B LEU* 4.0 26.7 - - + -
83B GLU* 4.1 7.2 - - - +
93B LYS* 2.9 34.7 + - + +
94B VAL 3.9 2.9 - - - +
96B LEU* 1.3 75.2 - - + +
98B HIS* 1.3 62.6 + - - +
100B PHE* 3.6 11.1 + - - +
101B HIS 5.1 0.3 + - - -
147B CYS 4.6 1.7 - - - +
148B ARG* 5.7 0.2 - - - -
151B GLY* 3.2 31.9 - - - +
154B MET* 3.3 32.5 - - + -
155B ALA* 3.9 28.7 - - + +
158B LEU* 4.1 12.8 - - + -
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Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 2.9 42.6 + - + +
95B PRO* 3.7 5.1 - - + +
97B LEU* 1.3 78.9 - - - +
99B ASN* 1.3 65.7 + - - +
101B HIS* 3.1 22.3 + - - -
148B ARG* 5.0 6.4 - - - +
151B GLY* 4.2 3.6 - - - -
152B ILE* 3.7 40.6 + - + +
155B ALA* 3.8 14.1 - - + +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PRO* 2.8 34.7 + - - +
96B LEU 3.9 0.9 - - - -
98B HIS* 1.3 80.5 - - - +
100B PHE* 1.3 66.9 + - - +
101B HIS* 3.2 11.8 - - - -
102B SER* 2.8 24.3 + - - +
103B PHE* 3.3 28.5 + - + -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.5 43.3 - - + -
78B ALA* 3.8 10.5 - - + -
79B LEU* 3.5 26.2 - - + -
82B LEU* 4.0 23.6 - - + -
96B LEU 3.1 15.6 + - - +
97B LEU 3.8 4.9 - - - +
98B HIS 3.4 1.8 - - - -
99B ASN* 1.3 76.7 - - - +
101B HIS* 1.3 64.6 + - - +
103B PHE* 3.0 31.1 + + - +
104B LEU* 3.5 11.3 + - + +
109B TRP* 4.4 9.2 - + - -
122B LEU* 4.8 0.2 - - + -
125B PHE* 3.5 37.5 - + - -
147B CYS* 4.0 15.9 - - + +
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU 5.1 0.2 + - - -
98B HIS 3.1 28.1 + - - -
99B ASN* 3.8 6.7 - - - -
100B PHE* 1.3 78.5 - - - +
102B SER* 1.3 80.7 + - - +
104B LEU* 3.4 28.1 - - - +
105B TYR* 3.5 14.9 - + - -
144B ALA* 3.4 30.5 - - + +
147B CYS* 4.2 4.7 - - - +
148B ARG* 3.7 40.0 - - + +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN* 2.8 15.3 + - - +
101B HIS* 1.3 100.3 + - - +
103B PHE* 1.3 58.1 + - - +
104B LEU 3.0 4.7 - - - -
105B TYR* 3.0 28.8 + - - +
106B GLN* 3.5 26.7 + - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PRO 5.2 0.2 - - - -
96B LEU* 3.7 33.4 - - + -
99B ASN* 3.5 29.8 - - + -
100B PHE* 3.0 22.6 + + + +
102B SER* 1.3 75.4 - - - +
104B LEU* 1.3 61.6 + - - +
105B TYR 3.1 0.4 - - - -
106B GLN* 3.1 43.2 + - - +
109B TRP* 3.2 71.0 - + + +
125B PHE* 4.0 12.4 - - + -
129B SER* 4.3 0.9 - - - -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.7 18.6 - - + -
100B PHE* 3.5 14.6 + - + +
101B HIS* 3.4 31.4 - - - +
102B SER 3.0 0.2 + - - -
103B PHE* 1.3 78.6 - - - +
105B TYR* 1.3 60.9 + - + +
125B PHE* 3.5 30.3 - - + -
129B SER* 3.4 18.4 - - - -
132B PHE* 3.5 46.1 - - + -
133B ARG* 3.6 4.9 + - - +
143B ILE* 4.6 1.1 - - + -
144B ALA* 4.0 22.2 - - + +
147B CYS* 4.3 11.9 - - - -
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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
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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