Contacts of the helix formed by residues 116 - 129 (chain B) in PDB entry 2VGZ
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 GLY 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B THR* 2.7 29.5 + - - -
115B SER* 1.3 75.6 - - - +
117B SER* 1.3 60.7 + - - -
118B GLN 3.3 2.5 - - - -
119B GLN 3.3 7.6 + - - -
270B ARG* 3.1 33.6 + - - -
271B ILE 4.0 2.5 - - - -
272B GLY* 3.8 9.9 - - - -
1263B PLP 3.7 2.5 - - - -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 4.0 6.5 - - - -
116B GLY* 1.3 68.9 - - - -
118B GLN* 1.3 66.4 + - - +
119B GLN 3.2 1.6 - - - -
120B GLY* 3.3 2.9 + - - -
121B LEU* 3.2 22.1 + - - +
230B ASP* 4.5 6.6 + - - -
232B PRO* 5.1 0.5 - - - +
258B ALA* 4.4 12.0 - - - +
259B ASP 3.3 35.7 - - - -
260B SER* 3.8 5.9 - - - -
272B GLY* 3.9 3.2 - - - -
273B PHE 4.8 1.8 - - - +
274B LEU* 6.4 0.2 - - - -
1263B PLP 2.8 34.9 + - - -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN 5.2 1.0 + - - -
290A VAL* 4.1 8.5 - - - +
291A SER 3.2 18.1 - - - +
293A LEU* 3.9 24.8 - - + +
117B SER* 1.3 73.5 + - - +
119B GLN* 1.3 63.8 + - - +
121B LEU* 3.7 18.6 - - - +
122B CYS* 3.0 26.3 + - - +
142B TYR* 2.9 45.5 + - - -
144B GLY* 5.2 3.2 - - - -
145B THR* 4.9 2.6 + - - -
1263B PLP 2.9 43.4 + - + +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A SER* 3.2 17.9 + - - +
292A THR* 4.0 12.1 - - + -
1426A IOD 3.6 6.8 - - + +
114B THR* 3.6 9.1 - - - -
115B SER* 3.0 34.5 + - - +
116B GLY 3.3 11.8 + - - +
117B SER 3.2 0.8 - - - -
118B GLN* 1.3 77.0 - - - +
120B GLY* 1.3 63.7 + - - +
122B CYS* 3.5 1.6 + - - +
123B LYS* 3.0 52.8 + - - +
288B ILE* 4.2 8.3 - - - +
292B THR* 2.8 42.7 + - - +
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Residues in contact with GLY 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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114B THR* 3.9 21.7 + - - -
116B GLY 4.0 2.8 + - - -
117B SER 3.3 6.6 + - - -
118B GLN 3.3 0.2 - - - -
119B GLN* 1.3 79.7 - - - +
121B LEU* 1.3 57.6 + - - +
123B LYS* 3.3 6.0 + - - +
124B VAL* 2.9 32.7 + - - +
274B LEU* 3.9 21.4 - - - +
284B VAL* 5.0 1.8 - - - -
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Residues in contact with LEU 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 SER 3.2 16.0 + - - +
118B GLN* 3.7 17.5 - - - +
119B GLN 3.2 0.2 - - - -
120B GLY* 1.3 76.1 - - - +
122B CYS* 1.3 57.1 + - - +
124B VAL* 3.1 8.8 + - + +
125B PHE* 2.8 50.7 + - + -
145B THR* 4.2 7.4 - - - +
195B TYR* 3.8 12.3 - - + -
228B ILE* 3.6 30.7 - - + -
230B ASP* 3.3 32.3 - - + +
258B ALA* 4.2 17.9 - - + -
274B LEU* 4.3 3.5 - - + +
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Residues in contact with CYS 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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287A HIS* 4.7 2.0 - - - -
290A VAL* 3.4 28.9 - - - +
291A SER* 3.8 19.1 - - - -
118B GLN 3.0 17.5 + - - +
119B GLN 3.7 3.1 - - - +
121B LEU* 1.3 76.9 - - - +
123B LYS* 1.3 57.9 + - + +
125B PHE* 3.4 11.8 + - - +
126B GLU* 2.9 53.4 + - - +
148B SER* 4.3 10.3 - - - +
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Residues in contact with LYS 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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291A SER* 6.4 0.4 - - - -
1426A IOD 3.5 13.5 - - - +
119B GLN* 3.0 50.0 + - + +
120B GLY 3.8 3.8 - - - +
122B CYS* 1.3 76.9 - - + +
124B VAL* 1.3 57.7 + - - +
126B GLU* 3.8 11.1 + - - +
127B MET* 2.9 30.0 + - - +
284B VAL* 4.1 20.6 - - + +
287B HIS* 3.3 43.3 + - + +
288B ILE* 3.6 24.0 - - + +
291B SER* 2.9 25.0 + - - -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 2.9 18.5 + - - +
121B LEU* 3.1 11.9 + - + +
123B LYS* 1.3 73.9 - - - +
125B PHE* 1.4 66.1 + - + +
127B MET* 3.3 15.2 + - + +
128B ILE* 3.3 40.9 + - + +
228B ILE* 3.9 23.3 - - + -
256B ILE* 4.0 26.5 - - + -
274B LEU* 3.9 14.8 - - + -
284B VAL* 3.9 17.0 - - + -
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Residues in contact with PHE 125 (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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121B LEU* 2.8 49.5 + - + -
122B CYS* 3.8 5.8 - - - +
124B VAL* 1.4 72.4 - - + +
126B GLU* 1.3 58.8 + - - +
128B ILE* 4.9 1.8 - - - -
129B ILE* 3.0 39.6 + - + +
145B THR* 3.9 24.5 - - + -
148B SER* 3.7 24.0 - - - +
149B LEU* 3.8 18.2 - - + -
152B LEU* 3.7 16.3 - - + +
193B PHE* 3.8 32.3 - + - -
195B TYR* 3.8 20.9 - + - -
228B ILE* 4.1 15.5 - - + -
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Residues in contact with GLU 126 (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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14A ARG* 4.3 6.2 + - - -
123A LYS* 5.8 0.2 + - - -
126A GLU* 4.7 3.4 - - - +
287A HIS* 2.9 32.7 + - - -
8B THR* 4.1 14.0 + - - +
122B CYS* 2.9 34.2 + - - +
123B LYS* 3.8 9.6 + - - +
125B PHE* 1.3 78.9 - - - +
127B MET* 1.3 61.0 + - - +
128B ILE 3.4 0.5 + - - -
129B ILE 4.1 7.2 + - - +
152B LEU* 4.3 22.9 - - + +
287B HIS* 3.4 29.2 + - + -
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Residues in contact with MET 127 (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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7B ILE* 3.3 19.4 - - + -
8B THR* 2.8 30.0 + - - +
11B SER* 3.5 22.3 - - - +
123B LYS 2.9 18.8 + - - +
124B VAL* 3.4 31.0 - - + +
126B GLU* 1.3 77.2 - - - +
128B ILE* 1.3 71.8 + - + +
256B ILE* 4.4 4.0 - - + -
280B LEU* 3.6 33.7 - - + +
283B ARG* 3.6 24.9 - - + -
284B VAL* 4.3 5.8 - - + +
287B HIS* 5.8 0.8 + - - -
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Residues in contact with ILE 128 (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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6B PHE* 3.2 24.9 - - + +
7B ILE* 4.6 1.8 - - + -
8B THR* 4.4 5.0 + - - -
124B VAL* 3.3 36.5 + - + +
125B PHE 4.1 1.6 - - - +
126B GLU 3.3 0.2 - - - -
127B MET* 1.3 94.9 - - + +
129B ILE* 1.3 73.1 + - + +
130B ASN* 3.5 0.9 + - - +
192B LYS* 2.9 59.5 + - + +
193B PHE* 3.9 17.7 - - + -
226B LEU* 4.3 17.3 - - + -
228B ILE* 4.3 4.5 - - + -
256B ILE* 4.6 0.9 - - + -
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Residues in contact with ILE 129 (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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8B THR* 3.8 7.5 + - - -
125B PHE* 3.0 20.9 + - + +
126B GLU* 4.1 6.1 + - - +
127B MET 3.8 0.4 - - - -
128B ILE* 1.3 82.6 - - + +
130B ASN* 1.3 73.8 + - - +
131B PRO* 4.6 2.1 - - - +
133B ASP* 4.1 10.5 - - + +
135B VAL* 3.5 30.7 - - + -
149B LEU* 4.9 2.0 - - + -
152B LEU* 3.7 42.2 - - + +
154B CYS* 3.8 16.6 - - + -
192B LYS* 4.6 1.3 - - + -
193B PHE* 3.6 21.3 - - + -
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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