Contacts of the helix formed by residues 120 - 131 (chain B) in PDB entry 4YVE
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 PHE 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B PHE* 4.0 16.8 - + - -
107B LEU* 4.0 20.6 - - + -
112B MET* 3.5 31.4 - - + -
117B ASP* 2.9 57.6 + - - +
118B SER* 4.2 2.2 - - - -
119B ALA* 1.3 77.9 - - - +
121B PHE* 1.3 78.2 + + + +
122B TRP 3.2 1.1 + - - -
123B GLU* 3.5 22.3 - - - +
124B GLU* 3.6 5.8 + - + +
217B PHE 3.9 3.1 - - - +
218B GLY* 3.5 35.7 - - - +
501B 4KK 5.3 5.4 - - - -
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Residues in contact with PHE 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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107B LEU* 4.0 22.2 - - + -
112B MET* 3.9 12.3 - - - -
118B SER* 3.2 34.8 - - - -
119B ALA 4.0 4.5 - - - -
120B PHE* 1.3 84.3 - + + +
122B TRP* 1.3 92.7 + + - +
123B GLU 3.6 0.2 - - - -
124B GLU* 3.6 12.0 - - + +
125B ARG* 3.0 29.3 + - - +
149B LEU* 3.8 14.8 - - + -
151B MET* 4.9 2.1 - - + +
393B PRO 3.5 16.4 - - - -
394B PHE* 3.7 24.9 - + - -
397B PHE* 3.8 24.6 - + + -
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Residues in contact with TRP 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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58A ARG* 3.3 51.3 - - - +
24B GLU* 5.8 2.5 - - - -
118B SER 4.7 0.4 + - - -
119B ALA* 3.0 39.5 + - + +
121B PHE* 1.3 94.4 - + - +
123B GLU* 1.3 68.1 + - - +
125B ARG* 3.0 22.1 + - - +
126B ASP* 2.9 37.6 + - - +
393B PRO 3.7 12.8 + - - -
394B PHE* 4.7 0.4 - - - -
395B VAL 3.6 11.2 - - - -
396B GLY 4.1 7.2 - - - -
397B PHE* 3.9 28.5 - - + -
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Residues in contact with GLU 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 ALA* 3.1 24.9 - - - +
120B PHE* 3.5 15.0 - - - +
122B TRP* 1.3 79.7 - - - +
124B GLU* 1.4 60.1 + - - +
126B ASP* 4.6 4.3 - - - +
127B ILE* 3.2 31.8 + - - +
194B PHE* 3.6 28.0 - - + -
217B PHE 4.3 0.9 - - - -
220B CYS* 3.2 33.5 - - + +
221B MET* 4.1 13.4 - - - +
222B LYS* 4.3 6.4 + - - +
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Residues in contact with GLU 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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105B LYS* 2.7 40.4 + - - +
107B LEU* 5.6 0.3 - - - +
120B PHE* 3.6 7.1 + - + +
121B PHE* 3.5 14.9 + - - +
122B TRP 3.1 0.8 - - - -
123B GLU* 1.4 77.6 - - - +
125B ARG* 1.4 60.7 + - - +
127B ILE* 4.2 0.9 - - - +
128B MET* 3.2 40.8 + - + +
151B MET* 3.6 21.2 - - + +
216B ASP* 3.4 10.2 + - - -
217B PHE* 2.8 55.2 + - - +
218B GLY* 4.5 2.2 - - - +
501B 4KK 4.8 0.3 - - - -
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Residues in contact with ARG 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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21B PRO 4.0 18.6 + - - -
22B LYS* 5.8 1.2 - - - +
23B SER 5.4 1.4 + - - -
29B CYS* 5.2 6.1 - - - -
121B PHE 3.0 13.5 + - - +
122B TRP* 3.3 20.1 - - - +
124B GLU* 1.4 75.7 - - - +
126B ASP* 1.3 70.6 + - - +
128B MET* 3.5 2.6 + - - +
129B ALA* 2.8 39.8 + - + +
130B PHE* 4.4 12.9 - - - -
139B LEU* 4.5 9.7 - - + +
142B ALA* 4.6 9.9 - - + -
151B MET* 4.8 7.0 - - - -
396B GLY 3.4 10.1 + - - -
397B PHE* 2.7 60.4 + - + +
398B THR 3.0 20.8 + - - -
399B TYR* 3.5 13.6 - - + +
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Residues in contact with ASP 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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122B TRP* 2.9 25.4 + - - +
123B GLU* 4.4 5.8 - - - +
125B ARG* 1.3 90.5 + - - +
127B ILE* 1.3 59.8 + - - +
130B PHE* 2.9 59.0 + - + +
192B MET* 4.6 3.0 - - - +
194B PHE* 4.9 10.1 - - + -
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Residues in contact with ILE 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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123B GLU 3.2 21.0 + - - +
124B GLU 4.2 2.0 - - - +
126B ASP* 1.3 75.8 - - - +
128B MET* 1.3 58.3 + - - +
131B ALA* 2.8 36.2 + - - +
136B VAL* 3.8 4.7 - - + -
189B ILE* 3.7 27.1 - - + -
192B MET* 3.9 13.2 - - + -
194B PHE* 3.5 52.0 - - + -
217B PHE* 3.8 22.0 - - + -
220B CYS* 3.9 23.1 - - + -
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Residues in contact with MET 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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124B GLU* 3.2 45.4 + - + +
125B ARG 4.0 0.4 - - - +
127B ILE* 1.3 77.6 - - - +
129B ALA* 1.4 61.6 + - - +
131B ALA* 4.3 4.0 + - - +
132B ASN 5.4 0.7 + - - -
136B VAL* 4.1 2.2 - - - -
137B VAL* 3.4 30.1 - - - +
138B GLN* 3.7 10.2 - - - +
139B LEU* 3.1 28.4 + - + +
151B MET* 3.8 17.9 - - + -
153B MET* 3.7 41.3 - - + +
215B ALA* 5.9 0.2 - - - -
216B ASP 5.8 1.1 - - - -
217B PHE* 3.6 20.2 - - + -
501B 4KK 5.4 2.5 - - + -
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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
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125B ARG* 2.8 26.7 + - + +
126B ASP 3.9 2.5 - - - +
127B ILE 3.3 0.2 - - - -
128B MET* 1.4 73.8 - - - +
130B PHE* 1.3 75.0 + - + +
132B ASN 5.5 0.2 + - - -
138B GLN* 5.7 1.7 - - - +
139B LEU* 3.6 31.0 - - + +
399B TYR* 3.6 30.2 + - + -
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Residues in contact with PHE 130 (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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21B PRO* 3.4 29.4 - - + -
22B LYS* 3.5 51.3 + - + -
125B ARG* 4.4 8.5 - - - -
126B ASP* 2.9 49.8 + - + +
129B ALA* 1.3 87.0 - - + +
131B ALA* 1.3 67.0 + - - +
132B ASN* 3.3 9.4 + - - +
192B MET* 4.5 5.8 - - + +
399B TYR* 3.6 30.5 - + - -
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Residues in contact with ALA 131 (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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127B ILE 2.8 25.3 + - - +
128B MET 4.3 2.4 + - - +
129B ALA 3.8 0.6 - - - -
130B PHE* 1.3 73.4 - - - +
132B ASN* 1.3 69.4 + - - +
133B SER* 3.3 5.9 + - - +
136B VAL* 3.6 31.6 - - + -
192B MET* 3.5 33.0 - - - +
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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
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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