Contacts of the helix formed by residues 120 - 136 (chain B) in PDB entry 4A8W
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PRO* 4.0 4.0 - - - +
119B VAL* 1.3 80.4 - - - +
121B GLU* 1.4 64.6 + - - +
122B ARG* 3.8 14.5 + - - +
123B ASP* 3.3 28.2 + - - +
124B ASN* 3.1 21.0 + - - +
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Residues in contact with GLU 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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120B SER* 1.4 70.7 - - - +
122B ARG* 1.3 54.3 + - - +
124B ASN* 3.2 29.5 + - - +
125B LEU* 2.9 61.9 + - + +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.8 10.9 + - - +
121B GLU* 1.3 76.5 - - - +
123B ASP* 1.4 82.2 + - - +
125B LEU* 3.1 14.7 + - - +
126B LEU* 2.9 35.4 + - + +
412B VAL* 4.0 5.7 + - - +
415B LEU* 3.5 31.3 + - - +
416B ASP* 2.6 33.5 + - - +
423B ASN* 2.7 47.9 + - + +
426B ILE* 3.9 29.1 - - + +
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 4.4 2.2 - - + -
119B VAL* 4.3 5.9 - - - +
120B SER* 3.3 19.3 + - - +
122B ARG* 1.4 99.7 + - - +
124B ASN* 1.3 60.2 + - - +
126B LEU* 3.2 7.9 + - - +
127B PHE* 3.0 42.1 + - + -
412B VAL* 3.5 21.5 - - + +
484B PRO* 5.1 1.0 - - - +
485B TYR* 2.6 38.9 + - + +
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Residues in contact with ASN 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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118B PRO* 3.7 21.0 - - + +
120B SER 3.1 13.6 + - - +
121B GLU* 3.2 36.6 + - - +
123B ASP* 1.3 74.7 - - - +
125B LEU* 1.3 60.4 + - - +
127B PHE* 3.6 2.3 + - - +
128B ARG* 2.8 64.2 + - - +
339B LEU* 3.6 12.2 - - - +
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Residues in contact with LEU 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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121B GLU* 2.9 44.8 + - + +
122B ARG* 3.1 7.6 + - - +
124B ASN* 1.3 77.0 - - - +
126B LEU* 1.3 53.1 + - - +
128B ARG* 3.4 2.8 + - - +
129B ALA* 2.7 35.5 + - - +
426B ILE* 4.4 13.5 - - + +
427B LYS 4.0 8.3 - - - +
428B ASP* 3.9 26.9 - - - +
429B MET* 3.7 40.6 - - + +
432B ALA* 4.1 12.1 - - + -
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Residues in contact with LEU 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 ARG* 2.9 28.7 + - + +
123B ASP 3.2 6.2 + - - +
125B LEU* 1.3 73.7 - - - +
127B PHE* 1.4 60.5 + - - +
129B ALA* 3.2 4.8 + - + +
130B ALA* 3.0 28.4 + - - +
408B ILE* 3.7 20.3 - - + +
411B LEU* 3.9 22.9 - - + -
412B VAL* 4.3 16.6 - - + -
415B LEU* 3.8 27.1 - - + -
426B ILE* 4.2 25.4 - - + -
432B ALA* 4.7 11.0 - - + +
435B PHE* 4.3 7.9 - - + -
436B LEU* 4.0 6.6 - - + +
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Residues in contact with PHE 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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118B PRO* 4.4 6.7 - - + -
123B ASP* 3.0 29.1 + - + +
124B ASN 4.0 0.2 - - - +
126B LEU* 1.4 73.3 - - - +
128B ARG* 1.4 63.2 + - - +
130B ALA* 3.3 13.0 + - - +
131B VAL* 3.4 17.0 + - - +
335B TRP* 3.8 28.9 - + - -
336B LEU* 3.8 22.4 - - + -
339B LEU* 3.8 22.9 - - + -
404B LEU* 4.1 7.0 - - + +
405B LEU* 4.0 20.4 - - + -
408B ILE* 3.6 36.3 - - + -
409B THR* 4.4 5.2 - - - -
485B TYR* 4.0 36.6 - + - -
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Residues in contact with ARG 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 ASN* 2.8 46.7 + - - +
125B LEU* 3.8 5.2 - - - +
127B PHE* 1.4 74.2 - - - +
129B ALA* 1.4 58.6 + - - +
131B VAL* 3.3 5.6 + - - +
132B ARG* 3.1 30.8 + - - +
339B LEU* 3.8 29.1 - - + +
342B ASP* 2.9 36.3 + - - +
343B GLU* 2.8 55.3 + - + +
346B ASN* 3.8 3.6 - - - +
429B MET* 3.8 16.2 - - - -
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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 LEU 2.7 21.4 + - - +
126B LEU* 3.2 10.7 + - - +
128B ARG* 1.4 69.6 - - - +
130B ALA* 1.4 60.4 + - - +
132B ARG* 3.5 1.6 + - - +
133B LEU* 3.0 34.5 + - - +
429B MET* 3.8 9.1 - - + +
432B ALA* 4.0 27.1 - - + +
433B CYS* 4.1 10.5 - - - -
436B LEU* 3.7 12.6 - - + -
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Residues in contact with ALA 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 LEU 3.0 12.5 + - - +
127B PHE 3.4 10.8 - - - +
128B ARG 3.3 0.2 - - - -
129B ALA* 1.4 73.1 - - - +
131B VAL* 1.4 58.4 + - - +
133B LEU* 3.5 0.5 + - - -
134B MET* 2.9 36.2 + - - +
404B LEU* 3.9 23.3 - - + +
408B ILE* 3.8 14.8 - - + -
436B LEU* 3.5 8.4 - - - +
440B TRP* 3.7 18.5 - - + -
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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
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127B PHE 3.5 15.0 - - - +
128B ARG* 3.3 9.1 + - - +
130B ALA* 1.4 73.7 - - - +
132B ARG* 1.3 56.8 + - - +
135B PHE* 2.9 42.6 + - + +
339B LEU* 4.6 2.2 - - + -
340B ILE* 3.8 35.7 - - + +
343B GLU* 3.9 23.3 - - + -
344B LEU* 3.8 30.7 - - + -
347B MET* 3.9 5.3 - - - +
404B LEU* 4.0 9.4 - - + -
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Residues in contact with ARG 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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128B ARG 3.1 16.3 + - - +
129B ALA 3.9 4.5 - - - +
130B ALA 3.4 0.2 - - - -
131B VAL* 1.3 76.6 - - - +
133B LEU* 1.3 53.9 + - + +
136B SER* 2.8 36.6 + - - -
343B GLU* 2.7 38.4 + - + +
346B ASN* 4.2 8.7 + - - +
347B MET* 3.6 52.1 + - + +
429B MET* 3.5 22.7 - - + +
433B CYS* 4.2 15.3 - - - -
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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
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129B ALA 3.0 17.4 + - - +
132B ARG* 1.3 77.9 - - + +
134B MET* 1.4 57.6 + - - +
136B SER* 4.0 2.7 - - - +
293B LYS* 2.8 32.6 + - - +
297B LYS* 5.6 2.5 - - - +
298B TYR* 3.6 26.8 - - + +
433B CYS* 3.7 27.1 - - + +
436B LEU* 3.8 21.8 - - + -
437B ASP* 3.5 33.0 - - + +
440B TRP* 3.7 17.0 - - + -
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Residues in contact with MET 134 (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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130B ALA 2.9 17.5 + - - +
133B LEU* 1.4 78.1 - - - +
135B PHE* 1.3 71.8 + - + +
136B SER 3.5 0.2 - - - -
138B LEU* 3.4 19.6 - - - +
290B VAL* 3.5 24.1 - - + +
293B LYS* 4.1 4.0 - - - +
294B ILE* 3.7 29.6 - - + -
302B PHE* 4.2 6.3 - - + -
400B LEU* 4.8 7.6 - - + +
403B THR* 4.1 26.5 - - + -
404B LEU* 3.7 36.3 - - + +
440B TRP* 3.7 28.9 - - + -
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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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131B VAL* 2.9 39.0 + - + +
134B MET* 1.3 85.4 - - + +
136B SER* 1.3 64.2 + - - +
138B LEU* 3.9 5.3 - - - +
286B VAL* 4.2 14.1 - - + -
287B ALA* 5.9 0.7 - - - -
290B VAL* 3.6 27.4 - - + -
340B ILE* 4.6 11.2 - - + -
344B LEU* 3.6 26.7 - - + -
347B MET* 3.7 6.0 - - + +
349B TYR* 2.7 45.0 + + + +
353B TRP* 4.7 10.1 - + - -
357B PHE* 5.0 6.1 - + - -
397B ALA* 6.2 0.9 - - + -
400B LEU* 5.2 5.8 - - + -
401B MET* 4.4 21.8 - - + -
404B LEU* 4.7 7.9 - - + -
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Residues in contact with SER 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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132B ARG 2.8 21.0 + - - -
133B LEU* 3.4 2.4 + - - +
134B MET 3.5 2.8 + - - -
135B PHE* 1.3 80.3 - - - +
137B ASP* 1.3 64.0 + - - -
138B LEU* 2.8 19.9 + - - +
293B LYS* 2.5 27.4 + - - +
347B MET* 4.1 8.5 - - - -
349B TYR* 4.7 0.2 + - - -
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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
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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