Contacts of the helix formed by residues 127 - 142 (chain A) in PDB entry 4M8J
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 SER 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A MET* 4.3 0.9 - - - +
124A GLU* 3.3 34.1 + - - -
125A GLY 3.1 3.0 + - - -
126A TYR* 1.3 78.9 - - - +
128A ALA* 1.3 63.6 + - - +
129A PRO* 3.3 16.0 - - - +
130A ALA* 2.9 33.7 + - - +
131A LYS* 3.1 17.9 + - - +
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Residues in contact with ALA 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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126A TYR 3.9 0.8 + - - -
127A SER* 1.3 68.3 - - - +
129A PRO* 1.4 75.2 - - + +
131A LYS* 3.0 16.4 + - - +
132A GLU* 2.9 33.5 + - + +
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Residues in contact with PRO 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET* 3.3 32.0 - - + +
124A GLU* 5.7 2.5 - - - +
127A SER* 3.3 14.4 - - - +
128A ALA* 1.4 94.1 - - + +
130A ALA* 1.3 56.9 + - - +
132A GLU* 3.6 23.8 - - - +
133A ILE* 3.4 15.9 + - - +
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Residues in contact with ALA 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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115A TYR 4.2 2.6 - - - +
116A ILE* 3.3 20.7 - - + +
119A PRO* 3.6 27.1 - - + -
123A MET* 3.9 7.2 - - - -
124A GLU 3.8 8.1 - - - +
127A SER* 2.9 24.7 + - - +
129A PRO* 1.3 75.0 - - - +
131A LYS* 1.3 61.2 + - - +
132A GLU 3.2 0.4 - - - -
133A ILE* 3.5 5.9 - - - +
134A GLY* 3.0 23.7 + - - -
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Residues in contact with LYS 131 (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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116A ILE* 3.5 23.1 - - + -
126A TYR* 3.3 34.1 + - - +
127A SER 3.1 15.2 + - - +
128A ALA* 3.0 12.5 + - - +
130A ALA* 1.3 74.3 - - - +
132A GLU* 1.3 62.6 + - - +
134A GLY* 3.9 1.6 - - - -
285A TYR* 2.4 38.8 + - + -
371A LEU* 4.5 16.8 - - + -
374A ILE* 6.2 2.5 - - - -
375A ASP* 3.5 26.9 + - - +
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Residues in contact with GLU 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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123A MET* 6.0 0.2 - - - +
128A ALA* 2.9 21.1 + - + +
129A PRO* 3.6 27.5 - - - +
131A LYS* 1.3 80.4 - - - +
133A ILE* 1.3 60.5 + - + +
134A GLY 3.2 1.3 + - - -
135A LEU 4.3 0.2 + - - -
136A ALA* 4.2 1.9 + - - +
285A TYR* 4.9 1.1 - - - -
288A ASP* 4.8 15.6 - - - +
289A SER* 3.6 19.2 + - - -
292A THR* 4.2 20.9 + - + +
296A TYR* 5.4 3.6 + - - -
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Residues in contact with ILE 133 (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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115A TYR* 5.1 2.0 - - + +
120A PRO* 4.2 20.2 - - + -
121A PHE* 4.2 13.7 - - + -
123A MET* 4.0 18.2 - - + -
129A PRO 3.4 12.0 + - - +
130A ALA* 3.5 11.4 - - - +
132A GLU* 1.3 77.7 - - + +
134A GLY* 1.3 68.0 + - - +
135A LEU 3.5 0.7 - - - -
136A ALA* 4.0 4.3 - - + -
137A TYR* 3.2 34.0 + - + +
292A THR* 3.7 21.5 - - + -
296A TYR* 4.3 15.5 - - + -
300A MET* 3.6 26.2 - - + -
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Residues in contact with GLY 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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112A ILE* 4.3 12.0 - - - +
115A TYR* 3.2 42.8 - - - -
116A ILE* 5.4 1.8 - - - -
130A ALA 3.0 17.4 + - - -
131A LYS* 3.8 1.7 + - - -
132A GLU 3.2 2.6 - - - -
133A ILE* 1.3 79.6 - - - +
135A LEU* 1.3 62.4 + - - +
137A TYR 3.6 1.4 + - - -
138A SER* 3.9 0.9 + - - -
285A TYR* 4.2 5.6 - - - -
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Residues in contact with LEU 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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112A ILE* 4.3 8.9 - - + +
132A GLU 4.3 0.4 + - - -
134A GLY* 1.3 69.8 - - - +
136A ALA* 1.3 58.6 + - - +
137A TYR 3.0 2.5 - - - -
138A SER* 2.7 36.1 + - - +
139A LEU* 3.1 22.1 + - + +
285A TYR* 3.4 43.1 + - + -
286A PHE* 4.1 12.6 - - - -
289A SER* 3.5 20.9 - - - +
363A TRP 3.6 24.2 - - - +
364A THR* 3.7 28.9 - - + +
367A GLY* 5.2 0.2 - - - -
368A GLY 4.7 5.4 - - - +
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Residues in contact with ALA 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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132A GLU 4.2 2.2 - - - +
133A ILE* 3.5 18.3 + - + +
134A GLY 3.4 0.6 - - - -
135A LEU* 1.3 77.5 - - - +
137A TYR* 1.3 59.2 + - - +
139A LEU* 3.5 8.1 + - - +
140A PHE* 3.4 18.7 + - - +
289A SER* 3.4 31.4 + - - +
292A THR* 3.9 14.1 - - + -
293A LEU* 3.7 24.3 - - - +
300A MET* 4.2 2.3 - - + +
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Residues in contact with TYR 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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115A TYR* 3.8 18.8 - + + -
120A PRO* 3.7 22.2 - - + -
121A PHE* 4.1 11.2 - + - -
133A ILE* 3.2 31.1 + - + +
134A GLY 3.8 1.1 - - - +
135A LEU 2.9 1.0 + - - -
136A ALA* 1.3 74.9 - - - +
138A SER* 1.3 61.9 + - - +
140A PHE* 3.2 14.7 + + - +
141A HIS* 3.0 66.1 + + - -
300A MET* 3.8 33.4 - - + +
303A TYR* 3.4 28.6 - - - +
312A PHE* 3.4 26.1 - + - -
317A THR* 4.0 4.1 + - - -
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Residues in contact with SER 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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111A GLU* 2.3 34.9 + - - +
112A ILE* 5.0 4.5 + - - +
115A TYR* 3.4 9.6 - - - -
134A GLY 4.3 1.6 + - - -
135A LEU* 2.7 21.7 + - - +
137A TYR* 1.3 70.0 - - - +
139A LEU* 1.3 59.8 + - - +
140A PHE 3.0 4.9 - - - -
141A HIS* 4.8 0.2 - - - -
142A TRP* 2.9 37.8 + - - +
360A TRP* 5.1 0.4 - - - -
363A TRP* 3.3 27.3 + - - -
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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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135A LEU* 3.1 33.0 + - + +
136A ALA* 3.6 9.9 - - - +
137A TYR 3.2 0.2 - - - -
138A SER* 1.3 78.5 - - - +
140A PHE* 1.3 57.1 + - - +
143A GLY* 3.2 12.9 - - - -
144A PRO* 4.2 1.4 - - - +
286A PHE* 4.3 9.0 - - + -
289A SER* 3.5 38.4 - - - +
290A VAL* 4.2 16.8 - - + +
293A LEU* 4.0 11.7 - - + +
297A MET* 5.3 0.2 - - - +
360A TRP* 2.9 51.7 + - + +
363A TRP* 5.1 3.1 - - + -
364A THR* 3.7 18.2 - - + -
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Residues in contact with PHE 140 (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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136A ALA 3.4 5.9 + - - +
137A TYR* 3.2 11.4 + + - +
138A SER 3.0 0.6 - - - -
139A LEU* 1.3 78.9 - - - +
141A HIS* 1.3 99.3 + + - +
142A TRP 3.2 1.3 - - - -
143A GLY* 3.7 0.9 + - - -
145A LEU* 4.0 27.2 - - + +
146A PRO* 3.4 21.1 - - - +
293A LEU* 3.6 17.0 - - + -
297A MET* 4.0 21.5 - - + -
300A MET* 3.6 37.2 - - + -
301A LEU* 3.6 31.0 - - + -
317A THR* 4.2 2.0 - - + -
321A TRP* 3.6 21.3 - + - -
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Residues in contact with HIS 141 (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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115A TYR* 2.8 26.5 + + - +
137A TYR* 3.0 36.6 + + - +
140A PHE* 1.3 98.7 - + - +
142A TRP* 1.3 73.1 + - + +
146A PRO* 3.1 17.7 - - - +
316A TRP* 4.2 3.6 - - + -
317A THR* 3.5 37.5 + - + +
320A TYR* 3.3 27.0 - + + -
321A TRP* 4.2 12.5 - + - -
324A TRP* 3.2 18.2 + - - -
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Residues in contact with TRP 142 (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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107A TRP* 4.8 8.1 - + - -
111A GLU* 2.6 26.3 + - - -
138A SER 2.9 25.6 + - - +
139A LEU 4.1 0.4 - - - -
141A HIS* 1.3 90.3 - - + +
143A GLY* 1.3 56.7 + - - +
147A TRP* 4.6 2.5 - - - -
320A TYR* 3.4 34.5 - + - -
323A TRP* 3.4 41.1 - + - -
324A TRP* 3.5 38.1 - + - -
359A THR* 2.9 30.5 + - + +
360A TRP* 3.6 8.6 - - + -
363A TRP* 3.2 56.8 - + + +
601A NM2 4.4 6.7 - - - -
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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