Contacts of the helix formed by residues 118 - 135 (chain B) in PDB entry 2YVC
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 PRO 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B TYR* 3.6 35.4 - - + +
117B CYS* 1.3 91.5 - - + +
119B PRO* 1.3 71.0 - - + +
120B GLU 3.6 1.8 - - - +
121B THR* 3.6 17.8 + - + +
122B ALA* 2.9 23.4 + - - +
157B VAL* 5.0 0.4 - - + -
160B GLN* 5.4 0.2 - - - +
198B LEU* 4.6 10.1 - - + -
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Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 5.0 1.1 - - - +
117B CYS 3.9 0.2 - - - -
118B PRO* 1.3 87.4 - - + +
120B GLU* 1.3 67.7 + - + +
122B ALA* 3.1 7.6 + - + +
123B VAL* 3.0 30.2 + - - +
157B VAL* 4.1 17.9 - - + -
160B GLN* 3.6 17.3 - - - +
161B HIS* 3.5 34.8 - - + +
168B TRP* 4.8 7.0 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 3.6 0.6 - - - +
119B PRO* 1.3 85.5 - - + +
121B THR* 1.3 62.2 + - - +
123B VAL* 3.4 3.6 + - - +
124B LEU* 3.3 19.6 + - - +
171B ARG* 2.8 36.8 + - - -
175B TRP* 4.8 8.7 + - - -
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B CYS* 3.7 16.2 - - - -
118B PRO* 3.6 23.1 + - - +
120B GLU* 1.3 76.3 - - - +
122B ALA* 1.3 58.0 + - - +
124B LEU* 3.3 10.3 + - + +
125B LEU* 2.9 29.7 + - + +
194B ILE* 3.8 26.9 - - + -
198B LEU* 4.2 13.1 - - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 5.9 0.7 - - + -
117B CYS* 3.5 17.9 - - - +
118B PRO 2.9 19.9 + - - +
119B PRO* 3.1 11.4 + - + +
121B THR* 1.3 75.1 - - - +
123B VAL* 1.3 65.2 + - - +
125B LEU* 3.6 4.6 + - - +
126B ALA* 3.0 22.5 + - - +
152B LEU 4.7 1.9 - - - +
153B LEU* 3.8 8.5 - - + +
154B PRO* 4.0 27.1 - - + +
157B VAL* 4.4 1.1 - - + -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO 3.0 13.9 + - - +
120B GLU 3.8 6.1 - - - +
121B THR 3.4 0.4 - - - -
122B ALA* 1.3 74.5 - - - +
124B LEU* 1.3 52.8 + - - +
126B ALA* 2.8 6.9 + - - +
127B SER* 2.8 31.2 + - - -
153B LEU* 3.8 13.9 - - + -
168B TRP* 3.7 30.7 - - + -
171B ARG* 4.3 22.9 - - + +
172B ILE* 3.5 30.9 - - + +
175B TRP* 3.8 19.3 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU 3.3 10.4 + - - +
121B THR* 3.3 12.1 + - + +
123B VAL* 1.3 75.9 - - - +
125B LEU* 1.3 66.2 + - - +
127B SER* 2.4 25.1 + - - +
128B TYR* 3.1 34.0 + - + +
175B TRP* 3.7 50.6 - - + +
179B HIS* 4.0 3.8 - - + -
194B ILE* 3.6 25.6 - - + -
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Residues in contact with LEU 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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110B ILE* 3.8 28.0 - - + -
117B CYS* 3.7 28.0 - - - -
121B THR* 2.9 22.7 + - + +
122B ALA* 3.6 5.6 - - - +
124B LEU* 1.3 71.0 - - - +
126B ALA* 1.3 65.0 + - - +
128B TYR* 3.0 17.8 + - - +
129B ALA 3.1 9.7 + - - -
191B TYR* 3.4 58.7 - - + +
194B ILE* 3.7 22.7 - - + -
195B ALA* 4.2 2.5 - - + +
198B LEU* 4.6 4.7 - - + -
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Residues in contact with ALA 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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107B LYS* 5.6 1.6 - - - +
122B ALA 3.0 14.4 + - - +
123B VAL 2.8 12.6 + - - +
125B LEU* 1.3 76.3 - - - +
127B SER* 1.3 55.7 + - - +
129B ALA* 3.1 9.7 + - - +
130B VAL* 2.8 31.7 + - - +
152B LEU* 3.7 30.2 - - + +
153B LEU* 4.6 0.4 - - + -
172B ILE* 3.8 23.3 - - + -
191B TYR* 5.1 1.1 - - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL 2.8 8.9 + - - -
124B LEU* 2.4 28.6 + - - -
126B ALA* 1.3 76.3 - - - +
128B TYR* 1.3 54.1 + - - +
130B VAL* 3.1 6.4 + - - +
131B GLN* 2.8 29.6 + - - +
172B ILE* 3.8 14.1 - - - +
175B TRP* 3.3 28.2 - - - +
176B HIS* 3.7 9.2 - - - +
179B HIS* 2.7 25.9 + - - -
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.2 39.6 - - + +
125B LEU* 3.0 10.4 + - - +
127B SER* 1.3 77.2 + - - +
129B ALA* 1.3 61.1 + - - +
131B GLN* 3.3 3.7 + - + +
132B ALA* 2.9 24.3 + - - +
179B HIS* 3.2 29.5 + + - -
182B MET* 3.8 21.0 - - + +
187B SER* 3.5 29.0 - - - +
190B GLU* 3.6 33.9 + - + +
191B TYR* 4.1 13.7 - - + -
194B ILE* 3.7 25.0 - - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 4.1 25.1 - - + -
107B LYS* 3.5 29.8 - - - +
125B LEU 3.1 10.6 + - - +
126B ALA* 3.4 8.7 - - - +
128B TYR* 1.3 74.7 - - - +
130B VAL* 1.3 65.2 + - + +
132B ALA* 3.0 5.0 + - - +
133B LYS* 2.9 25.0 + - - +
152B LEU* 6.0 1.6 - - + -
191B TYR* 4.2 6.6 - - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 2.8 16.3 + - - +
127B SER* 3.1 9.8 + - - +
129B ALA* 1.3 75.7 - - - +
131B GLN* 1.3 56.1 + - - +
133B LYS* 3.0 3.2 + - - -
134B TYR* 2.9 44.1 + - + +
146B TYR* 4.2 5.8 - - - +
147B LEU* 3.8 31.0 - - + -
150B ASP* 5.7 0.4 - - - +
152B LEU* 4.1 16.2 - - + -
172B ILE* 3.9 9.2 - - + -
176B HIS* 3.3 40.2 - - + +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B SER 2.8 15.8 + - - +
128B TYR* 3.6 9.9 - - - +
130B VAL* 1.3 73.1 - - - +
132B ALA* 1.3 56.4 + - - +
135B GLY* 2.9 50.6 + - - -
136B ASP* 3.2 22.5 - - - +
137B TYR 4.3 1.0 - - - +
176B HIS* 3.2 26.2 + - + -
179B HIS* 3.7 34.5 + - + +
182B MET* 3.0 24.6 + - + +
184B ARG* 3.8 3.3 - - - -
187B SER* 3.2 17.9 - - - +
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Residues in contact with ALA 132 (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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103B PHE* 4.8 4.0 - - + -
128B TYR 2.9 11.8 + - - +
129B ALA* 3.0 8.0 + - - +
131B GLN* 1.3 75.6 - - - +
133B LYS* 1.3 57.1 + - - +
184B ARG* 3.3 36.4 + - - +
187B SER* 3.4 24.9 - - - -
188B MET* 3.9 20.2 - - + +
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Residues in contact with LYS 133 (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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15A GLU* 2.9 42.5 + - - +
129B ALA 2.9 14.0 + - - +
130B VAL* 3.0 4.0 + - - +
132B ALA* 1.3 81.1 - - - +
134B TYR* 1.3 89.9 + - + +
135B GLY 3.4 0.7 - - - -
149B ASN 5.3 0.6 + - - -
150B ASP* 2.7 30.9 + - - +
184B ARG* 3.5 20.7 + - - +
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Residues in contact with TYR 134 (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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130B VAL* 2.9 29.7 + - + +
133B LYS* 1.3 110.7 + - + +
135B GLY* 1.3 64.8 + - - +
136B ASP 3.8 5.9 + - - +
142B HIS* 3.8 32.8 - + + -
146B TYR* 3.6 19.3 + + + -
147B LEU* 3.8 20.4 - - + -
150B ASP* 2.8 26.6 + - - -
176B HIS* 4.4 5.4 - - + -
184B ARG* 4.1 7.0 + - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 2.9 28.2 + - - +
134B TYR* 1.3 76.8 - - - +
136B ASP* 1.3 66.9 + - - +
176B HIS* 3.1 19.1 + - - -
182B MET 5.5 1.3 - - - -
184B ARG* 3.3 23.0 - - - +
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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
------------------------------------------------------------
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