Contacts of the helix formed by residues 125 - 140 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU 4.3 2.5 - - - +
124B LEU* 1.3 96.5 - - + +
126B GLU* 1.3 65.6 + - - +
127B ASP* 3.4 21.5 - - - +
128B VAL* 2.9 32.6 + - + +
129B LEU* 3.0 11.1 + - - +
42C ARG* 5.9 0.7 - - - -
46C PHE* 4.2 12.6 - - + -
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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
----------------------------------------------------------
124B LEU 3.4 3.2 + - - -
125B PRO* 1.3 71.8 - - - +
127B ASP* 1.3 58.0 + - - +
129B LEU* 3.3 8.3 + - - +
130B ASP* 2.9 29.8 + - + +
1246B GOL 3.6 23.2 + - - +
142C ARG* 5.4 8.2 + - - +
213C ARG* 5.8 1.6 + - - -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.4 18.4 - - - +
126B GLU* 1.3 79.4 + - - +
128B VAL* 1.3 61.9 + - - +
130B ASP* 3.5 1.1 + - - -
131B VAL* 3.2 22.5 + - - +
42C ARG* 2.0 49.1 + - - +
141C SER* 3.3 17.6 + - - +
142C ARG* 3.8 23.3 - - - +
245C LEU* 3.7 17.9 - - + +
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Residues in contact with VAL 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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61B ASN* 5.3 0.2 - - - +
67B ASP* 3.7 39.9 - - + +
124B LEU* 4.4 12.8 - - + -
125B PRO* 2.9 23.1 + - + +
127B ASP* 1.3 76.0 - - - +
129B LEU* 1.3 61.1 + - - +
131B VAL* 3.3 3.5 + - - +
132B GLN* 2.9 30.5 + - + +
42C ARG* 3.3 38.6 - - - +
46C PHE* 3.7 19.7 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.9 20.2 - - + -
118B SER* 5.5 1.6 - - - +
119B TYR 3.7 14.1 - - - +
120B GLY* 3.8 12.8 - - - +
121B ASN 3.4 38.8 - - - +
122B PRO* 5.1 2.2 - - + -
124B LEU* 3.9 24.7 - - + +
125B PRO 3.0 11.7 + - - +
126B GLU* 3.6 8.7 - - - +
128B VAL* 1.3 75.2 - - - +
130B ASP* 1.3 58.3 + - - +
132B GLN* 3.2 3.4 + - - -
133B LEU* 2.9 37.1 + - + +
1246B GOL 3.7 22.9 - - - +
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Residues in contact with ASP 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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126B GLU* 2.9 19.7 + - + +
127B ASP* 3.7 1.8 - - - +
129B LEU* 1.3 77.6 - - - +
131B VAL* 1.3 56.7 + - - +
133B LEU* 3.5 2.1 + - - +
134B ALA* 2.9 32.2 + - - +
137B ARG* 5.3 6.3 + - - -
1246B GOL 3.6 21.9 + - - -
140C SER 4.8 0.5 - - - +
141C SER* 2.8 40.2 + - - +
142C ARG* 5.9 0.7 - - - +
213C ARG* 4.2 14.8 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 3.9 17.5 - - + +
127B ASP 3.2 8.8 + - - +
128B VAL 3.7 2.7 - - - +
130B ASP* 1.3 76.0 - - - +
132B GLN* 1.3 64.4 + - - +
134B ALA* 3.1 7.5 + - - +
135B PHE* 3.0 32.8 + - + -
42C ARG* 3.3 26.7 - - - +
138C LEU 4.1 1.3 - - - +
139C LEU* 3.2 46.2 - - + +
140C SER* 3.8 5.4 - - - +
141C SER* 3.8 15.0 - - - +
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Residues in contact with GLN 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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58B VAL 4.7 0.2 + - - -
59B ASP* 2.8 27.7 + - - +
60B PRO* 3.3 23.8 - - + +
61B ASN* 2.8 41.9 + - - +
67B ASP* 3.0 26.6 + - - +
68B ALA* 4.2 1.6 - - - +
69B ILE* 4.2 26.0 - - + -
128B VAL* 2.9 24.5 + - + +
129B LEU 3.7 4.3 - - - +
131B VAL* 1.3 77.4 - - - +
133B LEU* 1.3 63.0 + - + +
135B PHE* 3.4 10.3 + - - +
136B LEU* 3.4 11.0 + - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 4.7 5.6 - - + -
82B ILE* 3.8 29.2 - - + -
119B TYR* 3.9 32.3 - - + +
120B GLY* 5.4 1.3 - - - -
129B LEU* 2.9 21.2 + - + +
130B ASP 3.8 3.8 - - - +
132B GLN* 1.3 77.1 - - + +
134B ALA* 1.3 52.2 + - - +
136B LEU* 3.2 7.9 + - - +
137B ARG* 2.8 48.9 + - - +
219B PRO* 4.3 18.6 - - + -
242B VAL* 5.5 1.1 - - + -
244B PHE* 4.6 7.8 - - + -
1246B GOL 3.3 30.3 - - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 2.9 22.0 + - - +
131B VAL* 3.1 10.5 + - - +
133B LEU* 1.3 72.9 - - - +
135B PHE* 1.3 62.0 + - - +
137B ARG* 4.1 19.7 - - - +
138B LEU* 2.9 43.2 + - + +
138C LEU* 4.3 15.3 - - + +
140C SER 5.6 3.4 - - - +
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Residues in contact with PHE 135 (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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135A PHE* 5.1 10.3 - + - -
139A LEU* 6.2 0.4 - - + -
60B PRO* 3.4 39.0 - - + -
61B ASN* 3.6 24.5 - - + -
131B VAL* 3.0 22.9 + - + -
132B GLN 3.7 2.2 - - - +
133B LEU 3.3 0.2 - - - -
134B ALA* 1.3 75.9 - - - +
136B LEU* 1.3 62.4 + - - +
139B LEU* 3.1 46.1 + - + +
39C ARG* 4.2 19.3 - - - -
135C PHE* 5.3 5.2 - + - -
138C LEU* 2.3 43.5 - - + -
139C LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 136 (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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40B ASN* 4.2 30.1 - - + +
60B PRO* 3.9 24.7 - - + -
69B ILE* 4.6 1.8 - - + -
80B THR* 4.4 12.8 - - + -
82B ILE* 3.6 30.5 - - + -
132B GLN 3.4 9.6 + - - +
133B LEU* 3.2 8.7 + - - +
135B PHE* 1.3 76.1 - - - +
137B ARG* 1.3 64.8 + - - +
139B LEU 5.3 0.2 - - - -
140B SER* 2.7 40.9 + - - +
244B PHE* 3.6 32.2 - - + -
245B LEU 5.7 1.1 - - - +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 5.3 6.7 + - - -
133B LEU* 2.8 37.4 + - - +
134B ALA* 3.9 18.6 - - - +
136B LEU* 1.3 72.0 - - - +
138B LEU* 1.3 69.4 + - + +
139B LEU 3.7 0.2 + - - -
140B SER 4.5 1.2 + - - +
174B SER* 3.5 24.3 + - - -
175B ASN* 4.8 1.4 + - - -
215B ALA* 3.4 19.7 + - - +
216B VAL* 2.8 57.8 + - - +
218B LEU 2.8 25.1 + - - +
219B PRO* 3.8 11.0 - - - -
244B PHE* 3.7 18.4 - - + -
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Residues in contact with LEU 138 (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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134A ALA* 4.8 5.0 - - - +
138A LEU* 3.9 36.7 - - + +
134B ALA* 2.9 34.1 + - + +
137B ARG* 1.3 89.5 - - - +
139B LEU* 1.3 63.8 + - + +
140B SER 3.7 2.8 + - - +
216B VAL* 4.2 27.1 - - + -
138C LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 139 (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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131A VAL* 3.5 27.4 - - - +
134A ALA* 3.8 33.4 - - - +
135A PHE* 3.6 46.3 - - + +
138A LEU* 3.6 28.0 - - + -
139A LEU* 4.3 10.1 - - + -
39B ARG* 5.4 2.3 + - - +
135B PHE* 3.1 36.3 + - + +
136B LEU* 4.1 0.7 - - - -
138B LEU* 1.3 82.0 - - + +
140B SER* 1.3 60.9 + - - +
138C LEU* 4.6 6.7 - - + -
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Residues in contact with SER 140 (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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131A VAL* 4.2 3.6 - - - -
134A ALA* 5.4 3.9 - - - +
40B ASN* 5.7 0.7 + - - -
136B LEU* 2.7 30.6 + - - +
137B ARG 4.5 0.9 + - - +
138B LEU 3.7 3.1 - - - +
139B LEU* 1.3 81.3 - - - +
141B SER* 1.3 63.5 + - - +
142B ARG 3.7 18.4 - - - -
213B ARG 4.9 3.5 - - - +
215B ALA* 4.3 9.9 + - - +
244B PHE* 3.3 21.8 - - - +
245B LEU* 3.8 14.2 + - - -
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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