Contacts of the helix formed by residues 125 - 142 (chain A) in PDB entry 5Y3A
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO 3.3 7.4 - - - +
124A ILE* 1.4 93.9 - - + +
126A PHE* 1.3 64.7 + - - +
127A SER* 4.4 7.9 - - - +
128A ASP* 3.2 43.7 + - - +
129A LEU* 3.5 4.7 + - - +
155E ASN* 5.7 2.0 - - - +
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Residues in contact with PHE 126 (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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124A ILE 3.5 2.6 + - - -
125A PRO* 1.3 69.4 - - - +
127A SER* 1.3 58.6 + - - +
129A LEU* 3.2 18.2 + - + -
130A GLN* 3.0 72.3 + - + +
204A SO4 3.1 44.4 - - - +
92D ARG 5.9 0.7 - - - +
93D GLY 4.9 10.1 - - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.2 6.0 - - - +
126A PHE* 1.3 78.5 + - - +
128A ASP* 1.3 64.0 + - - +
130A GLN* 3.6 11.9 + - - +
131A GLN* 3.2 23.4 + - - +
134A ARG* 4.8 2.4 + - - -
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.1 12.3 - - + -
125A PRO* 3.2 31.6 + - - +
127A SER* 1.3 80.1 - - - +
129A LEU* 1.3 56.0 + - - +
131A GLN* 3.4 4.9 + - - +
132A VAL* 3.3 27.9 + - - +
155E ASN* 5.0 7.1 + - - -
157E MET* 4.0 18.7 - - - +
170E LYS* 3.0 44.5 + - - +
171E MET 4.7 2.6 - - - +
201E SO4 4.8 4.2 + - - -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.8 39.0 - - + +
125A PRO 3.5 8.5 + - - +
126A PHE* 3.2 27.0 + - + +
128A ASP* 1.3 73.2 - - - +
130A GLN* 1.3 60.6 + - - +
132A VAL* 3.4 13.9 - - - +
133A SER* 3.1 19.1 + - - -
204A SO4 4.4 4.3 - - - +
69D VAL* 3.7 45.8 - - + -
146E VAL* 3.9 16.9 - - + +
148E CYS* 3.8 12.8 - - - -
157E MET* 4.6 3.1 - - - -
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 3.0 63.0 + - + +
127A SER* 3.9 9.4 + - - +
129A LEU* 1.3 75.6 - - - +
131A GLN* 1.3 60.2 + - - +
132A VAL 3.4 0.2 - - - -
133A SER* 3.2 8.8 + - - -
134A ARG* 3.0 41.2 + - - +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 3.2 12.1 + - - +
128A ASP 3.4 8.9 + - - +
130A GLN* 1.3 79.5 - - - +
132A VAL* 1.3 57.9 + - - +
134A ARG* 3.2 32.8 + - - +
135A ILE* 2.9 42.7 + - + +
97E ASN* 3.4 13.8 - - - +
100E ILE* 3.9 13.5 - - - +
157E MET* 5.7 0.7 - - - +
168E VAL* 5.6 1.4 - - - +
170E LYS* 2.8 29.1 + - - +
201E SO4 2.6 27.6 + - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP 3.3 11.0 + - - +
129A LEU* 3.4 20.4 - - - +
131A GLN* 1.3 77.7 - - - +
133A SER* 1.3 58.6 + - - +
135A ILE* 3.7 9.3 - - - +
136A ALA* 2.9 29.8 + - - +
146E VAL* 3.9 22.4 - - + -
157E MET* 3.7 35.7 - - + +
159E GLN* 3.9 10.1 - - + +
166E VAL* 4.2 10.7 - - + +
168E VAL* 3.8 20.4 - - + -
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.1 13.7 + - - -
130A GLN* 3.2 13.5 + - - -
131A GLN 3.2 0.4 - - - -
132A VAL* 1.3 78.3 - - - +
134A ARG* 1.3 62.1 + - - +
136A ALA* 3.6 2.9 - - - +
137A ALA* 3.3 21.7 + - - +
146E VAL* 4.7 1.9 - - - +
159E GLN* 2.9 30.2 + - - +
161E HIS* 4.8 2.6 - - - -
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 4.8 3.0 + - - -
130A GLN* 3.0 25.5 + - - +
131A GLN* 3.5 43.4 - - - +
133A SER* 1.3 72.2 - - - +
135A ILE* 1.3 67.1 + - + +
137A ALA* 3.2 6.4 + - - +
138A TYR* 3.1 43.0 + - + -
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Residues in contact with ILE 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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131A GLN* 2.9 38.7 + - + +
132A VAL* 3.7 5.2 - - - +
134A ARG* 1.3 76.0 - - + +
136A ALA* 1.3 61.6 + - - +
139A ALA* 3.0 12.3 + - + +
90E HIS* 3.0 37.5 + - + +
94E THR* 3.9 32.1 - - + +
100E ILE* 4.4 8.7 - - + -
103E VAL* 4.5 14.4 - - + -
166E VAL* 4.5 9.9 - - + -
168E VAL* 4.0 30.1 - - + -
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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 VAL 2.9 19.1 + - - +
133A SER 3.6 7.0 - - - +
135A ILE* 1.3 76.9 - - - +
137A ALA* 1.3 56.3 + - - +
139A ALA* 3.6 2.4 + - - +
140A TYR* 3.1 27.5 + - - +
159E GLN* 4.1 17.9 - - + +
161E HIS* 4.0 23.0 - - + +
164E ILE* 4.3 2.8 - - - +
166E VAL* 3.7 24.2 - - + +
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Residues in contact with ALA 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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133A SER 3.3 10.4 + - - +
134A ARG* 3.2 10.4 + - - +
136A ALA* 1.3 77.0 - - - +
138A TYR* 1.3 63.1 + - + +
140A TYR* 3.2 5.7 + - - +
141A SER* 3.1 27.8 + - - -
161E HIS* 3.8 22.9 - - + +
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Residues in contact with TYR 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 ARG* 3.1 39.5 + - + +
137A ALA* 1.3 78.6 - - + +
139A ALA* 1.3 60.4 + - - +
141A SER* 3.1 12.8 + - - -
142A ALA* 3.0 29.1 + - - +
90E HIS* 3.3 31.5 - + + +
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Residues in contact with ALA 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 ILE* 3.0 19.5 + - + +
136A ALA 3.9 4.0 - - - +
138A TYR* 1.3 77.1 - - - +
140A TYR* 1.3 61.0 + - - +
142A ALA* 3.6 3.7 + - - +
143A LEU* 3.3 29.1 + - - +
87E LEU* 3.8 18.4 - - + +
90E HIS* 3.5 16.3 - - + -
91E LEU* 5.3 0.2 - - + -
105E CYS* 4.0 5.4 - - - -
164E ILE* 4.8 3.6 - - + -
166E VAL* 4.0 20.2 - - + -
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Residues in contact with TYR 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 3.1 15.3 + - - +
137A ALA 3.2 8.5 + - - +
139A ALA* 1.3 75.2 - - - +
141A SER* 1.3 67.6 + - - +
143A LEU* 3.2 29.5 + - + +
144A SER* 4.0 2.4 + - - -
161E HIS* 4.0 22.9 - + - +
162E ASP* 3.3 42.5 + - + -
164E ILE* 3.5 28.5 - - + +
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Residues in contact with SER 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 ALA 3.1 14.1 + - - -
138A TYR* 3.1 22.9 + - - -
140A TYR* 1.3 79.4 - - - +
142A ALA* 1.3 56.8 + - - +
143A LEU 3.1 2.5 - - - -
144A SER* 2.6 29.8 + - - +
145A GLN* 4.2 4.7 + - - +
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Residues in contact with ALA 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 TYR 3.0 18.5 + - - +
139A ALA* 3.6 10.8 - - - +
140A TYR 3.2 0.4 - - - -
141A SER* 1.3 75.5 + - - +
143A LEU* 1.3 60.1 + - - +
144A SER 3.4 0.2 - - - -
145A GLN* 3.7 16.9 + - - +
146A ILE* 4.0 7.4 - - - +
83E MET 4.8 0.5 - - - +
86E THR* 3.8 25.4 - - + +
87E LEU* 3.7 32.4 + - - +
90E HIS* 5.0 3.1 - - + -
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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