Contacts of the helix formed by residues 129 - 148 (chain W) in PDB entry 5IY6
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 ASP 129 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127W GLY 5.1 1.6 - - - -
128W LYS* 1.3 79.4 + - - +
130W VAL* 1.4 57.8 + - + +
131W ASP* 3.7 13.4 - - + +
132W GLY* 3.0 40.8 + - - -
133W LYS* 3.3 11.1 + - - -
341W LYS* 6.1 0.2 - - - -
394W PHE* 2.8 43.3 + - - +
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Residues in contact with VAL 130 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W ARG* 2.9 32.4 + - + +
113W LYS* 4.1 28.3 - - + +
120W GLU* 3.8 25.4 - - - +
128W LYS 4.0 0.2 + - - -
129W ASP* 1.4 66.7 - - - +
131W ASP* 1.4 66.5 + - + +
133W LYS* 3.4 10.1 + - - +
134W CYS* 3.5 11.4 + - - -
211W TYR* 5.6 5.6 - - - +
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Residues in contact with ASP 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129W ASP* 3.7 12.0 - - + +
130W VAL* 1.4 76.6 - - + +
132W GLY* 1.3 64.5 + - - +
134W CYS* 3.2 19.2 + - - +
135W HIS* 3.2 37.6 + - - -
397W LEU* 5.7 5.2 - - - +
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Residues in contact with GLY 132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128W LYS* 5.8 2.9 - - - -
129W ASP* 3.0 30.3 + - - -
131W ASP* 1.3 74.5 - - - +
133W LYS* 1.3 52.4 + - - +
135W HIS* 3.2 10.5 + - - +
136W SER* 2.8 37.3 + - - -
341W LYS* 3.4 13.8 + - - -
394W PHE* 5.3 4.9 - - - -
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Residues in contact with LYS 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W ARG* 3.3 21.5 - - - +
113W LYS* 5.1 0.2 - - - +
119W PRO* 3.4 30.8 - - + +
120W GLU* 2.8 40.3 + - - +
123W PRO* 3.8 8.5 - - + +
128W LYS* 3.1 53.7 + - + +
129W ASP 3.3 14.0 + - - -
130W VAL* 3.9 5.9 - - - +
131W ASP 3.3 0.4 - - - -
132W GLY* 1.3 72.6 - - - +
134W CYS* 1.3 57.4 + - - +
136W SER* 3.3 8.9 + - - +
137W LEU* 2.9 30.4 + - - +
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Residues in contact with CYS 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W ARG* 3.4 40.6 - - - +
130W VAL 3.5 10.8 - - - -
131W ASP* 3.2 10.5 + - - +
133W LYS* 1.3 73.4 - - - +
135W HIS* 1.3 56.4 + - + +
137W LEU* 3.2 5.5 + - - +
138W THR* 2.7 38.2 + - - -
192W TYR* 5.2 4.0 - - - -
193W PHE* 3.8 28.0 - - + -
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Residues in contact with HIS 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131W ASP* 3.2 47.7 + - - -
132W GLY* 3.2 12.3 + - - +
134W CYS* 1.3 79.2 - - + +
136W SER* 1.3 56.7 + - - +
138W THR* 3.3 7.6 + - - -
139W ALA* 3.0 29.2 + - - +
341W LYS* 4.3 8.5 - - - +
342W TRP* 3.8 23.3 - + + -
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Residues in contact with SER 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128W LYS* 5.4 1.0 - - - +
132W GLY 2.8 10.1 + - - -
133W LYS* 3.4 13.8 - - - +
134W CYS 3.3 0.2 - - - -
135W HIS* 1.3 73.9 - - - +
137W LEU* 1.4 64.9 + - - +
139W ALA* 3.2 7.6 + - - +
140W SER* 3.0 19.2 + - - -
154W HIS* 6.3 0.2 - - - -
341W LYS* 2.8 24.2 + - - +
345W ARG* 3.1 31.7 - - - +
346W VAL* 3.7 16.1 - - - -
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Residues in contact with LEU 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112W ARG* 6.3 0.7 - - - -
119W PRO* 5.7 11.4 - - + -
133W LYS 2.9 16.7 + - - +
134W CYS* 3.7 5.8 - - - +
136W SER* 1.4 71.2 - - - +
138W THR* 1.4 66.0 + - - +
140W SER* 2.8 24.2 + - - +
141W TYR* 3.0 8.1 + - - +
154W HIS* 3.6 32.5 - - + +
156W ARG* 4.0 13.5 - - + +
157W PHE* 3.8 29.6 - - + +
190W CYS* 3.8 33.9 - - + -
193W PHE* 3.9 16.4 - - + -
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Residues in contact with THR 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134W CYS 2.7 24.2 + - - -
135W HIS* 3.5 9.2 + - - +
137W LEU* 1.4 74.5 - - - +
139W ALA* 1.4 57.3 + - - +
141W TYR* 3.2 4.5 + - + +
142W VAL* 3.0 39.0 + - + +
157W PHE* 4.2 18.4 - - + -
193W PHE* 3.7 14.6 - - - -
342W TRP* 4.1 15.9 - - + -
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Residues in contact with ALA 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135W HIS 3.0 14.3 + - - +
136W SER* 3.2 11.4 + - - +
138W THR* 1.4 72.4 - - - +
140W SER* 1.4 55.4 + - - +
142W VAL* 3.4 3.5 + - - +
143W ARG* 2.9 39.7 + - - +
342W TRP* 3.7 53.5 + - + +
345W ARG* 4.0 7.6 - - + -
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Residues in contact with SER 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136W SER 3.0 8.9 + - - -
137W LEU* 2.8 17.9 + - - +
139W ALA* 1.4 73.1 - - - +
141W TYR* 1.3 52.5 + - - +
143W ARG* 3.9 2.9 - - - +
144W ALA* 2.7 39.7 + - - +
152W LEU 3.4 21.0 - - - +
153W PRO* 3.9 1.1 - - - +
154W HIS* 3.0 28.7 + - - +
157W PHE 5.6 0.5 + - - -
345W ARG* 3.3 25.9 - - - +
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Residues in contact with TYR 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137W LEU 3.0 3.8 + - - +
138W THR* 3.2 8.0 + - + +
140W SER* 1.3 81.2 + - - +
142W VAL* 1.4 62.0 + - + +
144W ALA* 3.9 4.8 - - - +
145W GLN* 2.9 63.1 + - + +
153W PRO* 5.5 0.4 - - - -
157W PHE* 3.4 83.8 - + + +
158W TYR* 3.8 20.1 + - - -
159W GLU* 5.5 1.4 - - - -
161W PHE* 4.4 12.1 - + - -
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Residues in contact with VAL 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138W THR* 3.0 20.5 + - + +
139W ALA* 3.6 9.4 - - - +
141W TYR* 1.4 83.1 - - + +
143W ARG* 1.3 66.8 + - + +
145W GLN* 3.8 13.5 - - - +
146W TYR* 3.1 23.3 + - + +
342W TRP* 4.3 22.7 - - + +
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Residues in contact with ARG 143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139W ALA* 2.9 23.5 + - - +
140W SER 3.9 2.2 - - - +
142W VAL* 1.3 72.7 - - + +
144W ALA* 1.3 66.1 + - - +
146W TYR* 3.2 5.8 + - + +
147W GLN 3.1 20.6 + - - -
148W HIS* 3.2 45.7 + - - +
152W LEU* 3.1 24.7 - - + +
342W TRP* 3.8 27.0 - - + +
343W ARG* 2.8 44.3 + - - +
345W ARG* 4.7 1.8 - - - -
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Residues in contact with ALA 144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140W SER 2.7 24.1 + - - +
141W TYR* 3.9 4.0 - - - +
143W ARG* 1.3 73.2 - - - +
145W GLN* 1.3 61.3 + - - +
147W GLN* 4.0 0.9 + - - -
148W HIS* 3.4 6.7 + - - +
149W ASP* 2.7 43.8 + - - +
152W LEU* 5.2 0.2 - - - +
153W PRO* 3.4 41.1 - - + -
157W PHE 6.0 0.2 - - - +
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Residues in contact with GLN 145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141W TYR* 2.9 50.2 + - + +
142W VAL* 3.8 14.2 - - - +
144W ALA* 1.3 76.3 - - - +
146W TYR* 1.3 68.5 + - - +
149W ASP* 5.2 2.7 - - - -
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Residues in contact with TYR 146 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142W VAL* 3.1 15.5 + - + +
143W ARG* 3.2 11.2 + - - +
144W ALA 4.2 0.2 - - - -
145W GLN* 1.3 83.2 - - - +
147W GLN* 1.3 93.2 + - + +
148W HIS* 5.0 9.2 - + - -
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Residues in contact with GLN 147 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143W ARG 3.1 0.8 + - - -
144W ALA 4.5 0.4 - - - -
146W TYR* 1.3 105.3 + - + +
148W HIS* 1.3 78.6 + - + +
150W THR* 5.5 1.0 + - - -
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Residues in contact with HIS 148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W ARG* 3.2 66.0 + - - +
144W ALA* 3.7 2.5 - - - -
146W TYR* 5.0 8.8 - + - -
147W GLN* 1.3 86.9 + - + +
149W ASP* 1.3 69.0 + - - +
150W THR* 3.1 6.1 - - - -
151W SER* 2.8 29.2 + - - -
152W LEU* 2.9 39.6 + - + +
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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
------------------------------------------------------------
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