Contacts of the helix formed by residues 89 - 104 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C THR 3.8 3.8 + - - -
88C ILE* 1.3 73.0 - - - +
90C VAL* 1.3 65.1 + - - +
91C GLU* 2.8 19.0 + - - -
92C LYS* 3.0 17.2 + - - +
93C LYS* 2.9 20.8 + - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C MET* 6.1 4.7 - - + -
88C ILE 3.4 4.8 + - - +
89C SER* 1.3 70.1 - - - +
91C GLU* 1.3 74.1 + - + +
93C LYS* 3.8 9.2 - - + +
94C VAL* 3.0 34.8 + - + +
158C LEU* 3.8 38.1 - - + +
159C ASP* 5.4 7.6 - - + -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER* 2.8 13.0 + - - +
90C VAL* 1.3 89.2 - - + +
92C LYS* 1.3 60.5 + - - +
94C VAL* 3.9 3.7 + - - +
95C PRO* 3.3 17.0 - - - +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 3.7 21.8 - - + -
89C SER* 3.0 15.7 + - - +
91C GLU* 1.3 77.8 - - - +
93C LYS* 1.3 67.4 + - - +
94C VAL 3.4 0.2 - - - -
95C PRO* 3.1 14.5 - - - +
96C LEU* 3.4 47.2 + - - +
111C PHE* 3.7 10.1 - - + -
113C GLU* 3.7 23.6 - - - +
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.1 26.9 - - + +
83C GLU* 3.1 21.5 + - - +
85C ASP 2.9 28.4 + - - -
86C MET* 4.0 12.9 - - - +
88C ILE* 3.6 30.9 + - + +
89C SER 2.9 13.9 + - - +
90C VAL* 3.5 8.4 - - + +
92C LYS* 1.3 76.3 - - - +
94C VAL* 1.3 66.8 + - - +
96C LEU* 2.9 23.8 + - + +
97C LEU* 3.0 22.4 + - + +
158C LEU* 3.7 29.7 - - + +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C VAL* 3.0 20.4 + - + +
91C GLU* 4.2 3.4 - - - +
93C LYS* 1.3 76.7 - - - +
95C PRO* 1.3 66.0 - - + +
97C LEU* 3.3 2.6 + - - +
98C HIS* 2.9 55.8 + - + +
155C ALA* 4.1 14.1 - - + +
158C LEU* 3.7 17.3 - - + -
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Residues in contact with PRO 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU 3.3 14.8 - - - +
92C LYS* 3.1 17.0 - - - +
94C VAL* 1.3 94.8 - - + +
96C LEU* 1.3 54.0 + - + +
98C HIS* 4.2 5.8 - - + +
99C ASN* 2.7 54.2 + - - +
103C PHE* 5.4 0.4 - - - -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 4.3 20.7 - - + +
88C ILE* 4.2 8.1 - - + -
92C LYS* 3.4 40.4 + - - +
93C LYS* 2.9 18.3 + - + +
95C PRO* 1.3 79.7 - - + +
97C LEU* 1.3 61.0 + - + +
100C PHE* 3.0 31.9 + - - +
103C PHE* 3.7 14.9 - - + -
109C TRP* 4.4 17.9 - - + +
111C PHE* 3.6 33.0 - - + -
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 3.6 26.6 - - + +
82C LEU* 4.1 9.0 - - + -
83C GLU* 3.9 26.2 - - + +
93C LYS* 3.0 20.2 + - + +
94C VAL 3.8 4.9 - - - +
96C LEU* 1.3 80.3 - - + +
98C HIS* 1.3 61.5 + - - +
100C PHE* 3.6 11.3 + - - +
101C HIS 5.1 0.2 + - - -
147C CYS 4.7 1.4 - - - +
151C GLY* 3.2 34.0 - - - +
154C MET* 3.9 24.2 - - + -
155C ALA* 4.1 6.3 - - + +
158C LEU* 3.9 34.1 - - + -
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Residues in contact with HIS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL* 2.9 42.2 + - + +
95C PRO* 3.7 7.4 - - + +
97C LEU* 1.3 78.7 - - - +
99C ASN* 1.3 62.9 + - - +
101C HIS* 2.9 27.2 + - - -
148C ARG* 5.0 3.6 - - - +
151C GLY 3.9 4.9 - - - -
152C ILE* 3.4 47.4 + - + +
155C ALA* 3.6 13.8 - - + +
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Residues in contact with ASN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PRO* 2.7 40.3 + - - +
96C LEU 3.9 0.2 - - - -
98C HIS* 1.3 75.1 - - - +
100C PHE* 1.3 56.0 + - - +
101C HIS* 3.1 7.2 - - - -
102C SER* 2.5 45.7 + - - +
103C PHE* 3.2 26.7 + - + -
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Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C VAL* 3.3 44.9 - - + -
78C ALA* 3.7 16.2 - - + -
79C LEU* 3.7 33.2 - - + -
82C LEU* 3.8 24.0 - - + -
96C LEU 3.0 15.0 + - - +
97C LEU 3.7 10.8 - - - +
98C HIS 3.4 1.4 - - - -
99C ASN* 1.3 75.1 - - - +
101C HIS* 1.3 64.2 + - - +
103C PHE* 3.0 33.2 + + - +
104C LEU* 3.5 6.5 + - + +
109C TRP* 4.6 7.0 - + - -
125C PHE* 3.5 30.5 - + - -
147C CYS* 4.0 10.1 - - + +
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Residues in contact with HIS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU 5.1 0.2 + - - -
98C HIS 2.9 29.2 + - - -
99C ASN* 3.0 8.8 + - - -
100C PHE* 1.3 78.3 - - - +
102C SER* 1.3 73.5 + - - +
104C LEU* 3.3 30.1 - - - +
105C TYR* 3.8 11.8 - + - -
144C ALA* 3.7 26.2 - - + +
147C CYS* 4.3 4.6 + - + +
148C ARG* 3.7 46.6 - - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ASN* 2.5 43.6 + - - +
101C HIS* 1.3 83.0 - - - +
103C PHE* 1.3 57.0 + - - -
104C LEU 3.1 2.7 - - - -
105C TYR* 2.9 27.3 + - - +
106C GLN* 3.4 29.6 + - - +
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 5.6 0.4 - - + -
95C PRO 4.8 0.4 - - - -
96C LEU* 3.7 33.0 - - + -
99C ASN* 3.6 25.8 - - + -
100C PHE* 3.0 23.3 + + - +
102C SER* 1.3 77.7 - - - +
104C LEU* 1.3 62.3 + - - +
106C GLN* 3.0 42.7 + - - +
109C TRP* 3.4 71.7 - + + +
125C PHE* 4.0 13.7 - - + -
129C SER* 4.0 2.3 - - - -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C VAL* 3.9 22.2 - - + -
100C PHE* 3.5 5.8 + - + +
101C HIS* 3.3 31.1 + - - +
102C SER 3.1 0.2 - - - -
103C PHE* 1.3 79.0 - - - +
105C TYR* 1.3 59.6 + - + +
125C PHE* 3.5 28.5 - - + -
129C SER* 3.6 10.4 - - - -
132C PHE* 3.6 35.2 - - + -
133C ARG* 3.1 27.4 + - - +
143C ILE* 4.7 0.4 - - + -
144C ALA* 4.1 22.7 - - + -
147C CYS* 4.2 15.0 - - - -
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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
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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