Contacts of the helix formed by residues 115 - 125 (chain B) in PDB entry 3AEF
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 LEU 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 4.0 11.7 - - - +
62B ARG* 4.1 24.1 - - - +
72B SER 6.1 0.9 - - - +
102B LEU* 4.5 11.7 - - + -
105B MET* 5.1 10.5 - - - -
113B PRO* 3.0 18.6 + - + +
114B ASP* 1.3 72.7 + - - +
116B SER* 1.3 63.8 + - - +
117B ASN 3.3 3.1 - - - -
118B PHE* 3.0 18.5 + - + +
119B TYR* 2.9 60.4 + - + +
161B CYS 5.1 4.5 - - - +
162B ALA* 3.8 28.3 - - + -
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Residues in contact with SER 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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198A GLU* 5.7 0.7 + - - -
114B ASP* 2.5 28.0 + - - -
115B LEU* 1.3 77.7 - - - +
117B ASN* 1.3 57.6 + - - +
119B TYR* 3.4 11.5 + - - +
120B ALA* 2.8 30.0 + - - +
11C GLU* 4.7 8.4 - - - +
15C PHE* 3.9 16.6 - - - -
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Residues in contact with ASN 117 (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 MET* 6.0 3.7 - - + +
114B ASP 5.6 0.2 - - - +
115B LEU 3.3 0.4 - - - -
116B SER* 1.3 76.3 - - - +
118B PHE* 1.3 67.4 + - - +
120B ALA* 3.5 4.2 - - - +
121B GLN* 2.9 30.5 + - - +
171B TYR* 3.8 10.3 + - - -
175B GLY* 3.1 28.1 + - - -
11C GLU 5.5 0.2 - - - -
12C MET* 3.3 32.7 - - - +
15C PHE* 3.6 43.4 - - + -
16C TRP* 4.2 6.8 + - - +
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Residues in contact with PHE 118 (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 MET* 6.1 2.7 - - - -
114B ASP 5.4 0.2 + - - -
115B LEU* 3.0 23.6 + - + +
117B ASN* 1.3 80.9 - - - +
119B TYR* 1.3 80.8 + + - +
121B GLN* 3.2 21.5 + - - +
122B TYR* 3.2 12.2 + - + +
160B LEU* 3.8 38.6 - - + -
162B ALA* 3.7 33.0 - - + -
165B SER* 3.7 15.0 - - - -
171B TYR* 3.9 18.0 + + - +
179B LEU 5.7 0.2 - - - -
182B ALA* 3.6 33.2 - - + -
183B VAL* 4.2 10.2 - - + +
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Residues in contact with TYR 119 (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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52A PHE* 3.4 64.7 - + + +
55A ARG* 3.1 28.4 + - - -
163A TYR* 4.8 6.3 + - - +
175A VAL* 5.7 2.9 - - + -
176A GLU* 6.1 1.8 - - - -
62B ARG* 5.4 6.2 + - - -
115B LEU* 2.9 49.2 + - + +
116B SER* 3.8 8.1 - - - +
118B PHE* 1.3 90.0 - + - +
120B ALA* 1.3 57.1 + - - +
122B TYR* 3.2 13.9 + + + +
123B LYS* 3.0 26.9 + - - +
160B LEU* 4.6 6.1 - - + -
11C GLU* 4.7 3.4 - - - +
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Residues in contact with ALA 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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116B SER 2.8 19.0 + - - +
117B ASN* 3.2 6.9 + - - +
119B TYR* 1.3 77.1 - - - +
121B GLN* 1.3 61.4 + - - +
123B LYS* 3.1 7.6 + - - +
124B SER* 3.0 17.5 + - - -
8C ALA* 3.4 19.9 - - - +
11C GLU* 3.6 36.1 + - + +
12C MET* 3.8 12.6 - - + +
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Residues in contact with GLN 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 ASN* 2.9 27.1 + - - +
118B PHE* 3.4 11.5 + - - +
120B ALA* 1.3 75.9 - - - +
122B TYR* 1.3 63.0 + - - +
124B SER* 2.7 27.7 + - - -
125B ILE 3.6 0.9 + - - -
171B TYR* 2.8 30.9 + - - -
175B GLY 3.0 24.1 - - - +
176B ASP 4.1 4.7 - - - +
178B TYR 3.4 13.8 - - - +
179B LEU* 3.8 30.4 + - + +
183B VAL* 3.6 20.6 - - + +
12C MET* 4.6 11.9 - - + -
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Residues in contact with TYR 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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52A PHE* 5.8 1.1 - + - -
160A HIS* 4.4 19.6 + - - +
163A TYR* 3.9 29.1 - + - -
164A GLY* 5.0 0.6 - - - -
167A LEU* 4.7 2.2 - - + -
118B PHE* 3.2 9.6 + - + +
119B TYR* 3.2 16.5 + + + +
121B GLN* 1.3 76.5 - - - +
123B LYS* 1.3 64.2 + - - +
125B ILE* 3.0 24.2 - - + +
127B PRO* 3.3 46.3 + - + +
160B LEU* 3.6 40.7 - - + +
183B VAL* 3.6 18.3 - - + +
186B GLN* 3.9 34.8 + - + -
190B TRP* 5.2 1.2 + - - -
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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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163A TYR* 6.0 0.7 - - - +
167A LEU* 3.8 55.2 - - + +
169A TYR 5.7 3.2 + - - -
173A TYR* 6.2 2.0 - - - -
119B TYR 3.0 12.5 + - - +
120B ALA 3.1 10.3 + - - +
122B TYR* 1.3 76.8 - - - +
124B SER* 1.3 61.3 + - - +
125B ILE 3.2 1.0 + - - -
126B GLU* 3.3 15.8 + - - +
127B PRO* 4.2 0.7 - - - +
128B TYR* 5.8 0.3 - - - -
6C THR* 2.8 31.4 + - - +
7C THR* 4.7 1.1 - - - +
8C ALA* 4.0 16.9 - - + +
11C GLU* 2.8 27.1 + - - +
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Residues in contact with SER 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 ALA 3.0 11.0 + - - -
121B GLN* 2.7 24.9 + - - -
123B LYS* 1.3 76.6 - - - +
125B ILE* 1.3 64.8 + - - +
126B GLU* 3.4 6.5 + - - +
179B LEU* 3.9 12.5 - - - +
205B LYS* 5.1 9.7 - - - +
8C ALA* 3.7 16.2 - - - -
12C MET* 5.6 6.1 - - - -
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Residues in contact with ILE 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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122B TYR* 3.0 22.0 - - + +
124B SER* 1.3 82.7 - - - +
126B GLU* 1.3 68.4 + - - +
127B PRO* 4.3 8.1 - - + -
179B LEU* 3.7 22.2 - - + -
183B VAL* 3.6 32.3 - - + +
186B GLN* 4.0 11.4 - - + +
187B ALA* 3.5 43.2 - - + +
190B TRP* 5.2 0.4 - - + -
202B ARG* 3.0 21.7 + - - +
205B LYS* 6.1 6.1 - - + -
206B LEU* 5.6 2.5 - - + -
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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