Contacts of the helix formed by residues 125 - 140 (chain A) in PDB entry 4AEJ
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 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 4.2 3.6 - - - +
124A LEU* 1.3 91.6 - - + +
126A GLU* 1.3 66.6 + - - +
127A ASP* 3.5 17.7 - - - +
128A VAL* 3.2 8.9 + - + +
129A LEU* 3.2 17.7 + - - +
42B ARG* 3.5 23.6 - - - +
46B PHE* 4.2 18.4 - - + -
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 6.5 0.7 - - - -
124A LEU 3.7 1.9 + - - -
125A PRO* 1.3 75.0 - - - +
127A ASP* 1.3 58.0 + - - +
129A LEU* 3.4 11.7 + - + +
130A ASP* 3.0 44.1 + - - +
142B ARG* 5.3 2.9 - - - +
213B ARG* 3.2 27.8 + - - -
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.5 17.2 - - - +
126A GLU* 1.3 78.1 + - - +
128A VAL* 1.3 66.0 + - - +
130A ASP* 3.3 6.8 - - - +
131A VAL* 3.1 32.9 + - - +
42B ARG* 3.0 34.5 + - - +
141B SER* 3.4 26.5 - - - +
142B ARG* 4.8 7.2 - - - +
245B LEU* 3.5 25.9 - - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN* 5.0 0.7 + - - +
67A ASP* 3.6 39.0 - - + +
124A LEU* 4.5 14.6 - - + -
125A PRO* 3.2 13.0 + - + +
127A ASP* 1.3 90.0 - - - +
129A LEU* 1.3 60.2 + - - +
131A VAL* 3.3 8.4 + - - +
132A GLN* 3.0 28.7 + - + +
42B ARG* 3.8 33.4 - - + +
46B PHE* 4.2 12.8 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.1 10.8 - - + -
118A SER* 6.4 1.1 - - - -
119A TYR 3.5 20.6 - - - +
120A GLY* 3.9 20.9 - - - +
121A ASN 3.6 25.8 - - - +
122A PRO* 5.1 2.2 - - + -
124A LEU* 3.9 32.3 - - + +
125A PRO 3.2 11.1 + - - +
126A GLU* 3.4 14.6 + - + +
128A VAL* 1.3 74.3 - - + +
130A ASP* 1.3 66.8 + - - +
132A GLN* 3.1 3.4 + - + +
133A LEU* 2.9 32.4 + - + +
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.0 37.6 + - - +
127A ASP* 3.3 11.2 - - - +
129A LEU* 1.3 75.7 - - - +
131A VAL* 1.3 57.3 - - - +
133A LEU* 3.4 5.6 + - - +
134A ALA* 2.8 30.0 + - - +
137A ARG* 5.4 1.0 + - - -
141B SER* 3.7 24.0 - - - +
142B ARG* 4.3 1.0 + - - -
213B ARG* 3.7 19.9 + - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 3.8 20.9 - - + +
127A ASP* 3.1 15.3 + - - +
128A VAL* 3.6 10.1 - - - +
129A LEU 3.2 0.2 - - - -
130A ASP* 1.3 74.1 - - - +
132A GLN* 1.3 66.8 + - - +
134A ALA* 3.2 6.4 + - - +
135A PHE* 3.0 36.7 + - + -
39B ARG* 4.2 9.6 - - - +
40B ASN* 6.0 0.2 - - - +
139B LEU 3.5 24.7 - - - +
140B SER* 4.2 0.9 - - - -
141B SER 3.8 17.9 - - - +
245B LEU* 4.1 10.1 - - - +
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Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 2.7 26.9 + - - -
60A PRO* 3.1 19.9 - - + +
61A ASN* 2.9 43.9 + - - +
67A ASP* 2.9 29.9 + - - +
68A ALA* 4.0 3.2 - - - +
69A ILE* 4.4 21.3 - - + +
128A VAL* 3.0 23.9 + - + +
129A LEU* 3.1 5.3 + - - +
131A VAL* 1.3 76.8 - - - +
133A LEU* 1.3 65.6 + - + +
135A PHE* 3.4 10.8 + - - +
136A LEU* 3.4 18.3 + - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 5.3 3.4 - - + -
82A ILE* 4.2 20.2 - - + -
119A TYR* 4.4 26.5 - - + +
120A GLY* 5.4 2.0 - - - +
129A LEU* 2.9 24.6 + - + +
130A ASP* 3.8 5.2 - - - +
132A GLN* 1.3 78.4 - - + +
134A ALA* 1.3 59.4 + - - +
136A LEU* 3.1 5.5 + - - +
137A ARG* 2.7 42.5 + - - +
219A PRO* 4.3 21.8 - - + -
242A VAL* 4.6 4.3 - - + -
244A PHE* 3.9 31.6 - - + -
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 2.8 21.7 + - - +
131A VAL* 3.2 9.4 + - - +
133A LEU* 1.3 72.3 - - - +
135A PHE* 1.3 55.3 + - - +
137A ARG* 3.8 19.5 - - - +
138A LEU* 2.8 38.2 + - + +
138B LEU 4.8 4.5 - - - +
139B LEU* 3.9 22.9 - - + +
140B SER 5.4 3.6 - - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 3.5 27.6 - - + -
61A ASN* 3.4 36.3 - - + +
131A VAL* 3.0 32.0 + - + -
132A GLN 3.6 8.5 - - - +
134A ALA* 1.3 77.7 - - - +
136A LEU* 1.3 60.3 + - - +
139A LEU* 3.2 45.8 + - + +
39B ARG* 3.8 15.7 - - - -
60B PRO 6.0 0.2 - - - -
135B PHE* 5.1 12.6 - + - -
139B LEU* 3.6 45.1 - - + -
39C ARG* 6.1 0.7 - - - -
135C PHE* 5.1 9.4 - + - -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 4.4 23.3 - - + +
60A PRO* 3.8 26.5 - - + -
69A ILE* 4.5 5.2 - - + -
80A THR* 4.7 10.5 - - + -
82A ILE* 3.5 32.5 - - + -
132A GLN 3.4 13.9 + - - +
133A LEU* 3.1 9.3 + - - +
135A PHE* 1.3 78.3 - - - +
137A ARG* 1.3 61.4 + - - +
140A SER* 2.7 41.1 + - - +
244A PHE* 3.7 28.6 - - + -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 5.4 1.0 + - - -
133A LEU* 2.7 31.4 + - - +
134A ALA* 3.8 19.3 - - - +
136A LEU* 1.3 73.9 - - - +
138A LEU* 1.3 62.9 + - - +
140A SER 4.5 0.7 + - - +
174A SER* 3.8 21.4 + - - -
175A ASN* 4.0 7.7 + - - -
215A ALA* 3.3 22.0 + - - +
216A VAL* 2.8 55.6 + - + +
218A LEU 2.9 27.5 + - - +
219A PRO* 4.0 10.1 - - - -
244A PHE* 3.8 16.8 - - + -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA* 2.8 21.9 + - + +
137A ARG* 1.3 74.6 - - - +
139A LEU* 1.3 77.2 + - + +
140A SER 3.7 3.0 + - - +
216A VAL* 4.1 17.9 - - + +
138B LEU* 3.9 38.6 - - + +
139B LEU* 3.6 27.1 - - + -
134C ALA* 4.6 6.1 - - - +
138C LEU* 4.5 6.7 - - + -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 5.5 1.5 + - - +
135A PHE* 3.2 36.7 + - + +
136A LEU* 4.0 0.9 - - - -
138A LEU* 1.3 96.1 - - + +
140A SER* 1.3 61.8 + - - +
135B PHE* 6.2 0.4 - - + -
139B LEU* 4.3 18.6 - - + -
131C VAL* 3.4 28.6 - - - +
134C ALA* 3.9 35.5 - - + +
135C PHE* 3.7 45.8 - - + +
138C LEU* 4.6 8.7 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN* 5.5 1.9 + - - -
136A LEU* 2.7 30.7 + - - +
137A ARG 4.5 0.6 + - - +
138A LEU 3.7 3.2 - - - +
139A LEU* 1.3 80.9 - - - +
141A SER* 1.3 63.7 + - - +
142A ARG 3.7 15.0 - - - -
213A ARG 4.9 2.8 - - - +
215A ALA* 4.4 9.2 - - - +
244A PHE* 3.4 22.1 - - - +
245A LEU* 3.6 16.7 + - - -
130C ASP 6.0 0.2 - - - -
131C VAL* 4.0 4.3 - - - -
134C ALA* 5.4 3.6 - - - +
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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