Contacts of the helix formed by residues 128 - 144 (chain A) in PDB entry 5I75
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 GLY 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A MET 3.2 12.2 + - - -
127A PHE* 1.3 80.2 - - - +
129A GLY* 1.3 65.8 + - - +
131A PRO* 3.5 2.0 - - - +
132A LEU* 3.4 28.9 + - - +
545A SER* 4.1 2.1 + - - -
548A PHE* 3.6 33.1 - - - -
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET 2.9 10.1 + - - -
125A ALA* 2.9 12.3 + - - -
128A GLY* 1.3 69.7 - - - +
130A ILE* 1.3 57.9 + - - -
132A LEU* 3.3 5.7 + - - +
133A PHE* 2.8 29.6 + - - +
333A ILE* 4.7 7.6 - - - -
334A PHE* 5.7 1.3 - - - -
337A LEU* 3.5 25.5 - - - +
339A PRO* 4.5 3.5 - - - +
548A PHE* 4.2 3.5 - - - -
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA* 2.6 36.9 + - + +
126A ILE* 3.9 10.1 - - + +
129A GLY* 1.3 70.8 - - - -
131A PRO* 1.3 59.2 - - + +
133A PHE* 4.3 4.0 - - + -
134A TYR* 2.9 33.4 + - + +
337A LEU* 4.3 8.3 - - + -
361A ALA* 5.5 2.0 - - + +
362A LEU* 5.3 15.7 - - + +
365A SER* 3.6 33.0 - - - +
366A VAL* 5.5 5.4 - - + +
537A TRP* 3.5 28.3 - - + -
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Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.6 2.0 - - - +
126A ILE 3.3 22.2 - - - +
127A PHE 3.4 16.6 - - - +
128A GLY 3.5 11.0 - - - +
130A ILE* 1.3 90.0 - - + +
132A LEU* 1.3 55.6 + - - +
134A TYR* 4.8 0.7 - - + -
135A MET* 2.9 33.8 + - - +
537A TRP* 4.2 12.8 - - + -
540A CYS* 3.6 19.1 - - + -
541A TRP* 3.0 22.4 + - + +
545A SER* 3.4 15.7 - - - +
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Residues in contact with LEU 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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128A GLY 3.4 19.4 + - - +
129A GLY* 3.3 3.1 + - - +
131A PRO* 1.3 73.8 - - - +
133A PHE* 1.3 61.0 + - - +
135A MET* 4.0 22.9 - - + +
136A GLU* 2.9 32.7 + - - +
334A PHE* 4.4 11.9 - - + -
339A PRO* 3.7 18.5 - - + +
505A ALA 5.5 0.4 - - - +
509A ALA* 4.2 16.2 - - + -
541A TRP* 6.0 0.2 - - + -
545A SER* 3.8 22.9 - - - -
548A PHE* 4.2 8.1 - - + -
549A LEU* 3.6 37.2 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.7 21.1 - - + -
96A ALA* 5.1 8.7 - - + -
129A GLY 2.8 18.1 + - - +
130A ILE* 3.3 5.8 + - + +
132A LEU* 1.3 77.5 - - - +
134A TYR* 1.3 57.1 + - - +
136A GLU* 3.8 1.9 - - - +
137A LEU* 2.9 42.3 + - + +
337A LEU* 3.6 37.7 - - + -
339A PRO* 4.1 8.2 - - + +
344A LEU* 3.6 25.6 - - + +
361A ALA* 3.6 23.8 - - + -
364A THR* 3.1 29.8 - - - -
365A SER* 3.6 18.6 - - - +
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Residues in contact with TYR 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 ILE* 2.9 16.5 + - + +
131A PRO* 4.3 1.3 - - + +
133A PHE* 1.3 74.8 - - - +
135A MET* 1.3 60.4 + - - +
137A LEU* 3.6 1.5 - - + -
138A ALA* 2.9 36.0 + - + +
357A CYS* 3.5 26.9 - - + -
358A TYR* 3.4 43.1 - + - -
361A ALA* 4.0 16.4 - - + -
521A PHE* 5.2 0.4 - + - -
525A VAL* 3.2 31.2 - - + +
529A LEU* 3.8 13.3 - - - +
533A PRO* 4.9 4.4 - - + +
537A TRP* 4.6 15.7 - + + -
541A TRP* 3.3 40.4 - + - -
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Residues in contact with MET 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO 2.9 21.8 + - - +
132A LEU* 4.0 26.9 - - + +
134A TYR* 1.3 78.1 - - - +
136A GLU* 1.3 66.3 + - + +
138A ALA* 3.6 1.4 + - - +
139A LEU* 3.4 35.8 + - - +
508A GLU* 5.4 1.6 - - + -
509A ALA* 4.5 18.2 - - + +
512A VAL* 3.7 30.5 - - + -
513A SER* 6.5 0.4 - - - -
518A ILE* 5.8 0.7 - - + -
521A PHE* 3.7 27.7 - - + -
541A TRP* 3.4 26.0 - - + +
545A SER* 6.2 0.2 - - - -
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Residues in contact with GLU 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 LEU 2.9 20.8 + - - +
133A PHE 3.8 2.5 - - - +
135A MET* 1.3 84.6 - - + +
137A LEU* 1.3 61.4 + - - +
138A ALA 3.4 0.2 + - - -
139A LEU* 3.7 6.5 + - - +
140A GLY 3.7 13.9 + - - -
339A PRO* 4.5 0.2 - - + -
340A GLY* 3.8 20.9 + - - +
341A PHE 4.0 0.2 + - - -
342A GLY* 3.2 32.7 + - - -
343A VAL 4.5 0.3 + - - -
344A LEU* 3.7 28.6 + - + +
345A LEU* 3.6 26.7 + - - +
508A GLU* 3.6 16.1 - - - +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.9 10.8 - - + -
133A PHE* 2.9 30.0 + - + +
134A TYR* 3.2 6.5 + - + +
136A GLU* 1.3 76.3 - - - +
138A ALA* 1.3 61.0 + - - +
141A GLN* 3.7 10.1 + - - +
344A LEU* 3.6 38.4 - - + +
347A PHE* 5.5 2.2 - - + -
348A ALA* 3.1 33.8 - - + +
357A CYS* 4.4 8.9 - - + +
360A ASP* 4.4 11.7 - - + -
361A ALA* 3.8 34.1 - - + +
364A THR* 5.9 0.7 - - + -
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Residues in contact with ALA 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 TYR* 2.9 20.3 + - + +
135A MET 4.0 0.2 - - - +
136A GLU 3.3 0.4 - - - -
137A LEU* 1.3 77.6 - - - +
139A LEU* 1.3 66.9 + - - +
140A GLY 3.2 0.2 - - - -
141A GLN* 3.1 4.5 + - - +
142A TYR* 2.9 25.5 + - - +
357A CYS* 4.5 20.9 - - + -
521A PHE* 4.0 24.7 - - + -
525A VAL* 4.6 11.7 - - + -
528A MET* 4.3 4.8 - - - +
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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
----------------------------------------------------------
135A MET* 3.4 23.0 + - - +
136A GLU* 4.2 6.1 - - - +
138A ALA* 1.3 76.6 - - - +
140A GLY* 1.3 56.0 + - - +
142A TYR* 4.5 2.2 - - + -
143A HIS* 2.9 56.9 + - + +
150A ILE* 3.9 10.1 - - + +
154A ILE* 5.9 2.7 - - + -
345A LEU* 3.8 16.8 - - + -
512A VAL* 3.7 39.3 - - + -
516A TYR* 5.2 5.8 - - + -
521A PHE* 3.6 28.5 - - + -
524A ASP* 5.7 0.9 - - + +
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Residues in contact with GLY 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 GLU 3.7 3.4 + - - -
137A LEU 4.0 0.4 + - - -
138A ALA 3.2 1.0 - - - -
139A LEU* 1.3 78.8 - - - +
141A GLN* 1.3 56.9 + - - +
144A ARG* 2.9 24.6 + - - -
145A ASN 5.1 0.9 - - - -
150A ILE* 5.0 1.3 - - - -
345A LEU* 3.3 39.9 - - - +
348A ALA* 3.9 2.7 - - - -
349A SER* 3.1 19.9 - - - -
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Residues in contact with GLN 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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137A LEU* 3.9 6.6 - - - +
138A ALA 3.1 5.6 + - - +
140A GLY* 1.3 76.4 - - - +
142A TYR* 1.3 61.6 + - - +
144A ARG* 3.7 12.6 - - - +
348A ALA* 3.2 31.8 - - + +
349A SER* 4.4 0.7 - - - +
351A ASN* 2.2 42.0 + - + +
352A LYS 2.9 21.9 + - - +
353A PHE* 4.2 8.5 - - - -
355A ASN* 3.0 17.6 + - - +
356A ASN 4.6 0.5 - - - +
357A CYS* 3.6 22.6 - - - +
360A ASP* 5.1 2.3 - - - +
528A MET* 3.7 17.6 - - + +
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Residues in contact with TYR 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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138A ALA 2.9 17.2 + - - +
139A LEU* 3.9 4.0 - - + +
141A GLN* 1.3 80.4 - - - +
143A HIS* 1.3 97.2 + + - +
144A ARG* 3.6 5.9 + - - +
353A PHE* 3.7 33.2 - + - -
516A TYR* 4.5 1.9 + - - -
520A GLN* 5.2 0.7 + - - -
523A ARG* 4.8 7.4 + - - -
524A ASP* 2.9 53.1 + - + -
527A GLU* 4.6 7.7 - - + +
528A MET* 3.5 28.5 - - + -
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Residues in contact with HIS 143 (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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139A LEU* 2.9 41.6 + - + +
142A TYR* 1.3 105.1 - + - +
144A ARG* 1.3 70.7 + - - +
145A ASN* 3.2 7.8 + - + +
150A ILE* 3.9 25.6 - - + +
153A LYS* 4.5 17.0 + - + -
154A ILE* 3.4 31.2 - - + +
516A TYR* 4.6 9.1 + + - -
524A ASP* 4.8 0.4 - - - -
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Residues in contact with ARG 144 (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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79A ARG* 6.0 2.5 - - - +
140A GLY 2.9 17.3 + - - +
141A GLN 3.7 19.3 - - - +
142A TYR 3.9 2.7 + - - +
143A HIS* 1.3 81.5 - - - +
145A ASN* 1.3 57.8 + - - +
349A SER* 3.1 38.0 + - - +
351A ASN 4.4 12.3 - - - -
353A PHE* 3.7 30.8 - - - +
452A ASP* 4.1 5.5 - - - +
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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
------------------------------------------------------------
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