Contacts of the helix formed by residues 114 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B SER 3.3 23.6 - - - +
80B GLY* 4.0 0.6 - - - -
81B ASP* 3.7 3.4 - - - -
109B PRO* 3.4 31.6 - - + +
110B ALA 3.4 3.4 + - - -
111B GLY 2.8 29.3 + - - +
112B SER* 4.1 2.8 - - - +
113B GLY* 1.3 76.8 - - - +
115B ALA* 1.3 53.1 + - - +
116B LEU 3.3 2.7 - - - -
117B ALA* 3.2 5.8 + - + -
118B ALA* 2.7 36.3 + - - +
134B LEU* 4.4 8.6 - - + +
269B GLY* 5.1 3.2 - - - -
270B SER* 4.7 12.1 + - - +
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Residues in contact with ALA 115 (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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81B ASP* 3.0 13.1 + - - +
114B ASN* 1.3 73.7 - - - +
116B LEU* 1.3 53.0 + - - +
118B ALA* 3.3 3.8 + - - +
119B SER* 2.7 41.7 + - - -
167B LEU* 3.7 16.2 - - + -
267B HIS 3.2 22.4 - - - +
268B LEU 3.3 23.3 - - - +
269B GLY* 3.9 10.6 - - - +
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Residues in contact with LEU 116 (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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81B ASP* 3.1 17.2 + - + +
84B MET* 3.8 26.7 - - + -
107B SER* 4.4 13.2 - - - +
115B ALA* 1.3 76.1 - - - +
117B ALA* 1.3 64.5 + - - +
119B SER* 3.1 5.0 + - - -
120B LEU* 3.0 32.8 + - + +
166B VAL* 4.1 16.8 - - + +
167B LEU* 3.9 8.2 - - + +
265B HIS* 3.2 41.5 - - + +
361B MET* 3.2 35.2 - - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASP* 4.6 0.2 + - - -
107B SER* 4.1 19.7 + - - +
109B PRO* 3.9 38.1 - - + -
114B ASN* 3.2 11.7 + - + +
116B LEU* 1.3 78.8 - - - +
118B ALA* 1.3 62.5 + - - +
120B LEU* 3.4 4.6 + - - +
121B ASN* 3.1 24.9 + - - +
134B LEU* 4.4 2.2 - - + -
138B CYS* 3.7 15.0 - - - -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN 2.7 20.6 + - - +
115B ALA 3.6 4.7 - - - +
116B LEU 3.2 0.2 - - - -
117B ALA* 1.3 74.6 - - - +
119B SER* 1.3 61.3 + - - +
121B ASN* 3.6 3.7 + - - +
122B HIS* 3.1 22.2 + - - +
128B GLN* 6.3 0.2 - - + -
129B VAL 5.8 0.2 - - - +
134B LEU* 4.2 10.5 - - + +
267B HIS* 4.1 11.8 + - + -
269B GLY 4.0 5.2 - - - +
270B SER* 3.3 38.1 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA 2.7 27.6 + - - -
116B LEU 3.1 5.4 + - - -
118B ALA* 1.3 74.5 - - - +
120B LEU* 1.3 56.9 + - - +
122B HIS* 3.2 2.9 + - - +
123B TYR* 2.9 52.9 + - - -
265B HIS* 3.3 18.4 - - - +
266B SER* 3.5 16.6 - - - -
267B HIS* 3.1 22.4 + - - +
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Residues in contact with LEU 120 (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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107B SER* 4.6 13.5 - - - +
116B LEU* 3.0 24.6 + - + +
117B ALA* 3.4 5.4 + - - +
119B SER* 1.3 72.8 - - - +
121B ASN* 1.3 64.9 + - - +
123B TYR* 3.5 28.2 + - + +
124B ALA* 3.2 23.0 + - - +
138B CYS* 5.6 2.5 - - - -
141B LEU* 3.7 16.5 - - + +
150B MET* 4.1 20.4 - - - -
265B HIS* 4.8 4.5 - - + -
361B MET* 3.8 32.5 - - + -
362B VAL 3.9 13.9 - - - +
363B SER* 4.4 13.7 - - - -
364B GLY 5.0 2.4 + - - -
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Residues in contact with ASN 121 (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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117B ALA 3.1 17.4 + - - +
118B ALA 3.7 4.3 - - - +
120B LEU* 1.3 76.9 - - - +
122B HIS* 1.3 63.2 + - - +
124B ALA* 3.4 7.8 + - - +
125B GLY 3.6 0.3 + - - -
126B TYR* 3.2 37.7 + - - +
127B GLU 3.0 23.8 - - - +
128B GLN* 4.6 1.7 - - - -
129B VAL* 4.0 4.9 + - - +
134B LEU* 3.6 19.7 - - + +
137B ASN* 3.0 44.0 - - - +
138B CYS* 4.6 4.5 - - - -
141B LEU* 4.4 6.2 - - - +
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Residues in contact with HIS 122 (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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118B ALA 3.1 8.4 + - - +
119B SER 3.3 8.3 - - - +
121B ASN* 1.3 77.3 + - - +
123B TYR* 1.3 61.2 + + - +
125B GLY* 2.7 27.7 + - - -
126B TYR 4.0 14.3 + - - -
128B GLN* 5.9 1.3 - - + -
266B SER* 3.8 14.7 + - - +
267B HIS* 3.6 27.8 - + + +
273B PHE* 3.5 35.4 - + - -
276B PRO 5.7 0.4 - - - -
278B GLY* 5.6 8.5 - - - -
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Residues in contact with TYR 123 (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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119B SER* 2.9 26.2 + - - -
120B LEU* 3.8 28.3 - - + +
121B ASN 3.5 0.2 - - - -
122B HIS* 1.3 82.6 - - - +
124B ALA* 1.3 59.2 + - - +
125B GLY 3.2 1.4 + - - -
150B MET* 4.7 0.7 - - + -
264B LEU 4.4 0.5 + - - -
265B HIS* 2.9 36.4 + + - +
266B SER* 3.1 31.1 + - - -
279B ARG* 3.5 65.5 - - + +
363B SER* 5.6 2.0 - - - -
364B GLY 3.6 20.5 - - - +
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Residues in contact with ALA 124 (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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120B LEU 3.2 16.2 + - - +
121B ASN 3.6 6.7 - - - +
122B HIS 3.0 0.6 - - - -
123B TYR* 1.3 76.4 - - - +
125B GLY* 1.3 59.7 + - - +
126B TYR* 3.5 15.9 + - + -
141B LEU* 3.8 27.1 - - + -
364B GLY* 3.9 17.7 - - - -
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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