Contacts of the helix formed by residues 114 - 124 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D SER 3.1 23.9 - - - +
80D GLY* 3.7 2.9 - - - -
81D ASP* 3.6 4.9 - - - +
109D PRO* 3.4 30.7 - - + +
110D ALA 3.7 2.9 + - - -
111D GLY 2.9 24.3 + - - +
112D SER* 4.4 0.4 - - - +
113D GLY* 1.3 79.0 - - - +
115D ALA* 1.3 58.3 + - - +
116D LEU 3.2 2.9 - - - -
117D ALA* 3.3 5.9 + - + +
118D ALA* 2.9 30.0 + - - +
134D LEU* 4.4 9.2 - - + +
269D GLY* 5.4 0.8 - - - -
270D SER* 4.5 13.1 + - - +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP* 2.7 19.0 + - - +
113D GLY* 4.5 0.4 - - - -
114D ASN* 1.3 75.1 - - - +
116D LEU* 1.3 51.0 + - - +
118D ALA* 3.7 4.0 - - - +
119D SER* 2.6 38.4 + - - -
167D LEU* 3.5 15.7 - - + -
267D HIS* 3.2 21.3 - - - +
268D LEU 3.4 23.1 - - - +
269D GLY* 4.2 9.5 - - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP* 3.0 17.1 + - - +
84D MET* 3.6 37.5 - - + -
107D SER* 4.3 7.9 - - - +
115D ALA* 1.3 80.1 - - - +
117D ALA* 1.3 57.0 + - - +
119D SER* 3.3 5.6 + - - -
120D LEU* 3.0 36.2 + - + +
166D VAL* 3.9 20.2 - - + +
167D LEU* 4.3 7.5 - - + +
265D HIS* 3.5 37.2 - - + +
359D PHE* 5.7 0.9 - - + -
361D MET* 3.7 32.8 - - + -
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ASP* 4.5 0.4 + - - -
107D SER* 4.3 17.3 + - - +
109D PRO* 3.9 24.5 - - + -
114D ASN* 3.3 11.1 + - + +
116D LEU* 1.3 76.7 - - - +
118D ALA* 1.3 59.7 + - - +
120D LEU* 3.3 10.7 + - - +
121D ASN* 2.8 31.4 + - - +
134D LEU* 4.3 2.0 - - + -
138D CYS* 3.8 24.4 - - - -
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASN 2.9 12.6 + - - +
115D ALA 3.7 4.5 - - - +
117D ALA* 1.3 76.3 - - - +
119D SER* 1.3 56.0 + - - +
121D ASN* 3.1 4.2 + - - +
122D HIS* 2.8 29.6 + - - +
128D GLN* 6.1 0.7 - - + -
129D VAL 5.7 0.4 - - - +
134D LEU* 4.2 12.9 - - + +
267D HIS* 4.0 12.9 + - + -
269D GLY 3.9 7.4 - - - +
270D SER* 3.4 37.7 - - - +
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ALA 2.6 24.4 + - - -
116D LEU 3.6 5.2 - - - -
117D ALA 3.3 0.2 - - - -
118D ALA* 1.3 76.3 - - - +
120D LEU* 1.3 56.7 + - - +
122D HIS* 3.1 4.5 + - - +
123D TYR* 2.8 41.1 + - - -
265D HIS* 3.4 26.0 - - - +
266D SER* 3.5 17.3 - - - -
267D HIS* 3.0 23.5 + - - -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D SER* 4.3 15.7 - - - +
116D LEU* 3.0 27.9 + - + +
117D ALA* 3.8 8.5 - - - +
119D SER* 1.3 76.4 - - - +
121D ASN* 1.3 62.6 + - - +
123D TYR* 3.3 19.4 + - + +
124D ALA* 3.1 24.3 + - - +
138D CYS* 5.7 2.5 - - - -
141D LEU* 3.9 12.2 - - + +
150D MET* 4.6 6.3 - - - -
265D HIS* 5.6 0.7 - - + -
279D ARG* 6.1 0.2 - - - +
361D MET* 3.7 39.7 - - + -
362D VAL 3.9 9.2 - - - +
363D SER* 3.6 32.0 - - - +
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Residues in contact with ASN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA 2.8 18.6 + - - +
118D ALA* 3.3 4.9 - - - +
120D LEU* 1.3 78.4 - - - +
122D HIS* 1.3 62.2 + - - +
124D ALA* 3.4 5.9 + - - +
125D GLY 3.6 0.2 + - - -
126D TYR* 3.1 48.4 + - - +
127D GLU 2.9 24.0 - - - +
128D GLN* 4.4 2.3 - - - -
129D VAL* 4.1 4.0 + - - +
134D LEU* 3.5 20.3 - - + +
137D ASN* 3.2 32.3 - - - +
138D CYS* 4.7 3.4 - - - -
141D LEU* 4.6 8.0 - - - +
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Residues in contact with HIS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ALA 2.8 6.4 + - - +
119D SER 3.3 7.4 - - - +
121D ASN* 1.3 74.1 + - - +
123D TYR* 1.3 77.9 + + - +
124D ALA 3.0 1.8 - - - -
125D GLY* 2.9 15.8 + - - -
126D TYR 4.3 11.9 - - - -
128D GLN* 6.2 0.2 - - - -
266D SER* 3.8 12.7 + - - -
267D HIS* 3.5 26.9 - + + -
273D PHE* 3.6 34.5 - + - -
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D MET* 4.7 10.7 - - - +
119D SER* 2.8 28.2 + - - +
120D LEU* 3.3 23.3 + - + +
122D HIS* 1.3 83.1 - + - +
124D ALA* 1.3 60.2 + - - +
125D GLY* 3.3 1.4 + - - -
150D MET* 4.7 1.6 - - + -
264D LEU 4.4 1.0 + - - -
265D HIS* 2.9 39.7 + + - -
266D SER* 3.1 37.3 + - - -
279D ARG* 3.6 64.6 - - + +
280D CYS 5.5 0.3 + - - -
363D SER* 5.7 5.8 - - - -
364D GLY 4.0 7.4 - - - +
1002D EDO 4.5 1.7 - - - -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU 3.1 15.8 + - - +
121D ASN 3.7 6.5 - - - +
122D HIS 3.0 1.2 + - - -
123D TYR* 1.3 76.4 - - - +
125D GLY* 1.3 58.3 + - - +
126D TYR* 3.5 14.2 - - + -
141D LEU* 3.8 29.2 - - + -
364D GLY 3.3 21.9 - - - +
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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