Contacts of the helix formed by residues 107 - 122 (chain F) in PDB entry 3ZXR
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 107 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 5.9 0.2 - - - +
26F CYS 4.6 2.9 + - - +
61F PHE* 4.8 0.7 - - - -
93F PHE 5.1 0.6 - - - +
94F PHE* 3.3 15.0 - - - +
95F VAL* 2.8 53.0 + - + +
104F TYR* 3.3 19.4 + - + +
106F ARG* 1.3 77.4 - - - +
108F PRO* 1.4 69.8 - - - +
109F ARG* 2.8 19.9 + - - +
110F ASN* 3.0 27.3 + - + +
111F ILE* 3.2 14.1 + - - +
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Residues in contact with PRO 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F CYS* 3.4 20.6 - - + +
27F ASP 3.3 16.2 - - - +
28F LEU* 4.2 9.0 - - + -
61F PHE* 4.5 0.7 - - + -
106F ARG 3.2 9.0 - - - +
107F ASP* 1.4 89.1 - - - +
109F ARG* 1.3 60.3 + - - +
111F ILE* 3.1 13.5 + - + +
112F ALA 3.2 8.7 + - - -
375F ASN* 3.3 32.5 - - - +
377F TYR* 3.3 28.0 - - + +
378F LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F CYS* 4.5 12.8 - - + +
32F MET* 5.1 1.8 - - - -
74F ASP* 2.7 27.9 + - - +
77F THR* 3.7 5.1 - - - +
92F ASN* 3.9 15.9 - - - +
93F PHE 3.3 32.3 + - - -
94F PHE* 3.5 40.6 - - + -
107F ASP* 2.8 17.0 + - - +
108F PRO* 1.3 72.1 - - - +
110F ASN* 1.3 60.2 - - - +
112F ALA* 3.5 3.5 + - - +
113F ARG* 3.2 20.6 + - - +
236F LEU* 4.1 8.3 - - + +
240F ASP* 2.8 38.1 + - - -
377F TYR* 3.6 36.4 - - + -
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F VAL 5.5 0.2 - - - +
103F PRO* 3.4 24.7 + - + +
104F TYR 3.0 26.1 + - - +
105F SER* 4.5 1.0 - - - +
107F ASP* 3.0 22.8 + - + +
109F ARG* 1.3 78.7 - - - +
111F ILE* 1.3 58.5 + - + +
113F ARG* 3.1 31.4 + - - +
114F LYS* 2.8 55.5 + - - +
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Residues in contact with ILE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 6.3 0.2 - - + -
105F SER 3.4 25.6 - - - +
106F ARG 5.4 0.4 - - - -
107F ASP 3.4 14.6 - - - +
108F PRO* 3.1 6.4 + - + +
110F ASN* 1.3 76.0 - - + +
112F ALA* 1.3 54.1 + - - +
114F LYS* 3.2 16.7 + - - +
115F ALA* 2.8 32.7 + - - +
377F TYR 5.0 0.4 - - - +
378F LEU* 3.7 22.9 - - + -
381F SER* 4.0 10.1 - - - +
442F VAL* 3.6 24.0 - - + +
443F PHE* 3.9 30.7 - - + -
447F LEU* 3.5 15.0 - - + -
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PRO 3.2 8.2 + - - +
109F ARG 3.7 3.4 - - - +
110F ASN 3.2 0.4 - - - -
111F ILE* 1.3 76.4 - - - +
113F ARG* 1.3 64.9 + - - +
115F ALA* 3.3 2.8 + - - +
116F GLU* 3.0 29.0 + - - +
235F LEU* 3.7 21.1 - - + +
236F LEU* 3.7 27.1 - - + -
377F TYR* 4.1 13.4 + - + -
381F SER* 3.4 13.6 + - - +
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Residues in contact with ARG 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.3 64.2 - - + +
95F VAL 5.3 0.4 + - - -
96F HIS* 3.9 9.9 + - - -
103F PRO* 3.8 21.9 - - - +
109F ARG 3.2 8.4 + - - +
110F ASN* 3.1 30.5 + - - +
112F ALA* 1.3 78.2 - - - +
114F LYS* 1.3 63.1 + - + +
116F GLU* 3.1 16.8 + - - +
117F ASN* 3.1 27.8 + - - +
236F LEU* 4.6 13.2 - - + +
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F SER* 4.6 6.7 + - - +
110F ASN* 2.8 41.0 + - - +
111F ILE* 3.5 21.7 - - - +
113F ARG* 1.3 77.0 - - + +
115F ALA* 1.3 64.0 + - - +
117F ASN* 3.2 9.3 + - - +
118F TYR* 2.9 24.6 + - - +
441F GLY 3.0 20.0 + - - +
442F VAL* 2.8 36.5 + - + +
444F THR* 4.0 14.3 - - - +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ILE 2.8 21.7 + - - +
112F ALA 3.5 6.3 - - - +
113F ARG 3.2 0.2 - - - -
114F LYS* 1.3 73.1 - - - +
116F GLU* 1.3 61.8 + - - +
118F TYR* 3.4 3.1 + - - +
119F LEU* 3.1 22.7 + - - +
235F LEU* 4.2 13.2 - - + -
381F SER* 3.6 26.5 - - - +
384F LEU* 3.9 11.6 - - + +
385F MET* 5.2 2.7 - - - -
442F VAL* 3.9 16.3 - - + +
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA 3.0 15.2 + - - +
113F ARG* 3.1 8.5 + - - +
115F ALA* 1.3 74.9 - - - +
117F ASN* 1.3 63.7 + - - +
119F LEU* 3.5 11.4 + - + +
120F ILE* 3.4 28.3 + - + +
126F ASP 5.0 0.9 - - - +
128F ALA* 6.0 2.0 + - + +
234F SER* 3.6 13.5 + - - -
235F LEU* 3.2 27.6 + - + -
236F LEU* 3.1 43.3 + - - +
237F HIS* 5.9 0.2 - - - -
384F LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ARG* 3.1 26.7 + - - +
114F LYS* 3.7 10.5 - - - +
116F GLU* 1.3 77.2 - - - +
118F TYR* 1.3 64.8 + - - +
120F ILE* 3.1 18.2 + - - +
121F SER* 3.0 21.9 + - - -
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Residues in contact with TYR 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LYS 2.9 16.5 + - - +
115F ALA 3.7 2.9 - - - +
117F ASN* 1.3 72.0 - - - +
119F LEU* 1.3 68.5 + - - +
121F SER* 2.8 29.9 + - - -
122F THR* 3.1 28.6 + - + +
385F MET* 3.7 29.2 - - + -
388F LEU* 4.0 18.2 - - + -
392F LYS* 3.3 20.9 + - - +
439F GLU* 3.5 25.7 + - + +
440F GLY* 3.8 32.3 - - - +
442F VAL* 3.6 14.6 - - + -
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ALA 3.1 13.1 + - - +
116F GLU* 3.6 11.9 - - + +
117F ASN 3.2 0.2 - - - -
118F TYR* 1.3 75.4 - - - +
120F ILE* 1.3 63.4 + - - +
122F THR* 2.8 23.9 + - - +
123F GLY 3.8 0.3 + - - -
125F ALA* 3.3 35.8 - - + +
126F ASP 4.0 3.1 - - - +
127F THR* 3.6 16.4 - - - +
128F ALA* 3.5 39.9 - - + +
281F LEU* 4.3 5.6 - - + -
384F LEU* 4.2 8.7 - - + -
388F LEU* 3.8 36.3 - - + -
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLU* 3.4 17.7 + - + +
117F ASN* 3.1 20.3 + - - +
119F LEU* 1.3 75.5 - - - +
121F SER* 1.3 64.3 + - - +
123F GLY* 3.2 15.6 + - - -
125F ALA 3.7 7.5 - - - +
126F ASP* 3.6 33.7 - - + +
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Residues in contact with SER 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ASN 3.0 12.1 + - - -
118F TYR* 2.8 31.8 + - - -
120F ILE* 1.3 77.4 - - - +
122F THR* 1.3 59.0 + - - +
123F GLY 3.6 0.2 + - - -
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Residues in contact with THR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F TYR* 3.1 39.0 + - + +
119F LEU* 2.8 19.8 + - - +
121F SER* 1.3 76.9 - - - +
123F GLY* 1.3 56.6 + - - +
124F ILE* 3.1 36.7 + - + +
388F LEU* 4.6 3.5 - - + +
392F LYS* 3.3 31.7 + - - +
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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