Contacts of the helix formed by residues 114 - 124 (chain F) in PDB entry 3VZC
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 ASN 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79F SER 3.0 29.9 + - - +
80F GLY* 3.8 9.0 - - - +
81F ASP* 3.6 5.0 - - - +
107F SER* 4.4 4.0 + - - -
108F LEU 4.0 2.1 - - - +
109F PRO* 3.2 39.5 - - + +
110F ALA 3.4 5.1 - - - +
111F GLY 3.4 19.4 + - - -
112F SER 3.8 3.6 + - - -
113F GLY* 1.3 74.9 - - - +
115F ALA* 1.3 57.3 + - - +
116F LEU 3.5 2.0 - - - -
117F ALA* 3.7 9.8 - - + +
118F ALA* 2.9 28.0 + - - +
134F LEU* 5.0 5.7 - - + +
270F SER* 4.6 12.2 - - - +
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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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81F ASP* 2.9 18.9 + - - +
113F GLY* 3.5 1.2 - - - -
114F ASN* 1.3 68.9 - - - +
116F LEU* 1.3 56.8 + - - +
118F ALA* 2.9 8.0 + - - +
119F SER* 2.8 39.2 + - - -
167F LEU* 3.7 15.5 - - + -
267F HIS* 3.5 16.4 - - - +
268F LEU 3.1 27.4 - - - +
269F GLY* 4.3 6.8 - - - +
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Residues in contact with LEU 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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81F ASP* 3.1 16.9 + - - +
84F MET* 3.6 34.5 - - + -
107F SER* 4.5 6.3 - - - +
115F ALA* 1.3 77.4 - - - +
117F ALA* 1.3 62.4 + - - +
119F SER* 3.3 5.6 + - - -
120F LEU* 3.1 32.2 + - + +
166F VAL* 3.7 30.3 - - + +
167F LEU* 3.8 23.7 - - + +
265F HIS* 3.9 16.2 - - + +
361F MET* 3.6 35.0 - - + -
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Residues in contact with ALA 117 (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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81F ASP* 4.3 0.4 + - - -
107F SER* 3.7 22.6 + - - +
109F PRO* 3.9 25.4 - - + -
114F ASN* 3.4 25.2 + - + +
115F ALA 3.2 0.6 - - - -
116F LEU* 1.3 79.9 - - - +
118F ALA* 1.3 60.2 + - - +
120F LEU* 3.7 5.8 + - - +
121F ASN* 3.3 17.2 + - - +
134F LEU* 4.7 2.0 - - + -
138F CYS* 3.6 18.7 - - - -
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Residues in contact with ALA 118 (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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114F ASN 2.9 16.8 + - - +
115F ALA* 2.9 6.3 + - - +
117F ALA* 1.3 74.5 - - - +
119F SER* 1.3 61.1 + - - +
121F ASN* 3.3 8.1 + - - +
122F HIS* 3.0 28.1 + - - +
134F LEU* 4.5 7.6 - - + +
267F HIS* 4.1 19.2 + - + -
270F SER* 3.6 30.7 - - - +
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Residues in contact with SER 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 2.8 21.8 + - - -
116F LEU 3.6 5.6 - - - -
118F ALA* 1.3 72.3 - - - +
120F LEU* 1.3 56.8 + - - +
122F HIS* 3.1 2.4 + - - +
123F TYR* 2.8 53.8 + - - -
265F HIS* 3.3 17.0 - - - +
266F SER* 3.6 15.3 - - - -
267F HIS* 3.2 26.4 + - - +
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Residues in contact with LEU 120 (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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107F SER* 4.5 15.5 - - - +
116F LEU* 3.1 25.1 + - + +
117F ALA* 3.9 6.3 - - - +
118F ALA 3.3 0.2 - - - -
119F SER* 1.3 75.9 - - - +
121F ASN* 1.3 61.1 + - - +
123F TYR* 4.1 20.0 - - + +
124F ALA* 3.3 23.4 + - - +
138F CYS* 5.7 2.0 - - - -
141F LEU* 3.7 16.4 - - + +
150F MET* 4.4 19.7 - - + -
265F HIS* 5.6 1.6 - - + +
361F MET* 3.9 26.5 - - + -
362F VAL 3.5 17.3 - - - +
363F SER* 3.7 23.7 - - - -
364F GLY 4.6 2.6 + - - -
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Residues in contact with ASN 121 (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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117F ALA 3.3 14.3 + - - +
118F ALA 3.3 9.0 + - - +
119F SER 3.2 0.4 - - - -
120F LEU* 1.3 74.9 - - - +
122F HIS* 1.3 66.6 + - - +
124F ALA* 3.5 8.5 + - - +
125F GLY 3.6 0.2 + - - -
126F TYR* 3.1 31.8 + - - +
127F GLU 2.9 25.6 - - - +
128F GLN* 4.6 2.1 - - - -
129F VAL* 4.4 2.8 + - - +
134F LEU* 3.7 21.3 - - + +
137F ASN* 3.0 45.0 + - - +
138F CYS* 4.7 3.1 - - - -
141F LEU* 4.7 3.8 - - - +
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Residues in contact with HIS 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 ALA 3.0 7.0 + - - +
119F SER 3.2 8.5 - - - +
121F ASN* 1.3 74.5 + - - +
123F TYR* 1.3 72.7 + + - +
124F ALA 3.0 4.5 - - - -
125F GLY* 2.9 18.2 + - - -
126F TYR 4.1 11.1 + - - +
128F GLN* 6.4 0.9 - - + -
266F SER* 3.6 13.7 + - - -
267F HIS* 3.5 30.1 - + + -
273F PHE* 3.4 35.0 - + - -
279F ARG* 6.3 2.5 - - + -
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Residues in contact with TYR 123 (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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119F SER* 2.8 29.9 + - - +
120F LEU* 4.1 21.3 - - + +
121F ASN 3.5 0.2 - - - -
122F HIS* 1.3 84.4 - + - +
124F ALA* 1.3 58.9 + - - +
125F GLY* 3.5 0.7 + - - -
150F MET* 4.6 1.1 - - + -
265F HIS* 2.8 51.9 + + - +
266F SER* 3.2 24.1 + - - -
279F ARG* 3.6 67.7 + - + +
280F CYS 5.6 0.2 + - - -
363F SER* 5.7 2.2 - - - -
364F GLY 3.5 11.8 - - - +
1002F EDO 4.0 5.3 + - - -
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Residues in contact with ALA 124 (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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120F LEU 3.3 17.8 + - - +
121F ASN 3.8 6.3 - - - +
122F HIS 2.9 1.0 + - - -
123F TYR* 1.3 79.8 - - - +
125F GLY* 1.3 57.1 + - - +
126F TYR* 3.6 18.3 - - + -
141F LEU* 4.1 10.5 - - + -
364F GLY* 3.6 30.2 - - - +
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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