Contacts of the helix formed by residues 123 - 136 (chain B) in PDB entry 5AIV
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 ASN 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.7 17.5 - - + -
101B CYS* 6.0 1.6 - - - -
118B GLU 4.0 3.6 - - - +
119B LEU* 3.2 30.1 + - - +
122B TYR* 1.3 91.6 - - - +
124B ALA* 1.3 67.6 + - - +
125B PRO 3.3 2.2 - - - -
126B HIS* 3.2 16.1 + - - +
127B LEU* 3.3 12.0 + - - +
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Residues in contact with ALA 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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98B PHE* 3.6 28.0 - - + -
119B LEU 2.8 9.9 + - - +
120B LEU* 3.5 20.9 - - + +
123B ASN* 1.3 72.3 - - - +
125B PRO* 1.4 69.4 - - + +
126B HIS 3.3 0.2 + - - -
127B LEU* 3.3 4.0 + - - +
128B MET* 3.1 31.3 + - + +
160B LEU* 5.3 1.6 - - + -
167B LEU* 3.8 18.4 - - + -
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU 3.3 18.6 - - - +
121B THR 3.4 22.0 - - - +
122B TYR 3.9 1.3 - - - +
123B ASN 3.5 5.4 - - - +
124B ALA* 1.4 87.7 - - + +
126B HIS* 1.3 63.9 + - + +
128B MET* 3.5 9.2 + - + +
129B GLN* 3.1 25.6 + - - +
164B LYS* 4.5 12.1 - - - +
167B LEU* 5.1 2.5 - - + +
171B HIS* 4.7 3.6 + - - +
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Residues in contact with HIS 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 TYR 3.0 26.2 + - - -
123B ASN* 3.2 8.4 + - - +
125B PRO* 1.3 79.5 - - + +
127B LEU* 1.3 60.7 - - - +
129B GLN* 3.2 9.9 + - + +
130B ASP* 2.9 38.4 + - - +
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Residues in contact with LEU 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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48A PHE* 4.8 5.2 - - + -
94B THR* 3.6 32.8 - - + +
95B LEU* 4.4 15.9 - - + -
98B PHE* 3.6 41.1 - - + -
123B ASN 3.3 9.6 + - - +
124B ALA* 3.7 7.9 - - - +
126B HIS* 1.3 79.6 - - - +
128B MET* 1.3 73.3 + - + +
130B ASP* 3.3 6.7 + - - +
131B LEU* 2.8 43.4 + - + +
160B LEU* 5.2 1.3 - - + -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 5.7 0.2 - - + -
124B ALA* 3.1 24.7 + - - +
125B PRO* 3.7 7.4 - - + +
127B LEU* 1.3 99.7 - - + +
129B GLN* 1.3 58.8 + - - +
131B LEU* 3.3 1.9 + - + -
132B ASP* 2.8 31.0 + - - +
153B TRP* 3.6 27.6 - - + -
160B LEU* 4.2 17.5 - - + -
167B LEU* 3.9 28.9 - - + +
168B LEU* 3.6 24.2 - - + -
171B HIS* 3.7 22.2 - - + +
174B LEU* 3.6 7.8 - - + +
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Residues in contact with GLN 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 PRO 3.1 14.3 + - - +
126B HIS* 3.2 14.6 + - + +
128B MET* 1.3 76.8 - - - +
130B ASP* 1.3 67.8 + - - +
132B ASP* 3.2 4.5 + - - +
133B THR* 3.1 51.7 + - - +
171B HIS* 3.7 22.2 - - + -
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Residues in contact with ASP 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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47A PRO* 3.4 26.8 - - - +
48A PHE* 3.7 32.8 - - + +
126B HIS* 2.9 25.3 + - - +
127B LEU* 3.6 7.8 - - - +
129B GLN* 1.3 79.6 - - - +
131B LEU* 1.3 56.0 + - - +
133B THR* 3.7 4.5 + - - -
134B TYR* 3.1 28.4 + - - +
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Residues in contact with LEU 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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48A PHE* 3.7 26.5 - - + -
91B ILE* 4.3 20.2 - - + -
94B THR* 5.1 2.7 - - + -
95B LEU* 3.9 13.0 - - + -
127B LEU* 2.8 40.7 + - + +
128B MET* 3.7 6.1 - - + +
130B ASP* 1.3 74.6 - - - +
132B ASP* 1.3 59.9 + - - +
134B TYR* 3.3 3.7 + - - +
135B LEU* 2.9 30.5 + - - +
141B LEU* 4.7 12.5 - - + +
153B TRP* 3.7 34.8 - - + -
174B LEU* 4.3 14.1 - - + +
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Residues in contact with ASP 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 MET 2.8 21.7 + - - +
129B GLN* 3.6 7.6 + - - +
131B LEU* 1.3 73.5 - - - +
133B THR* 1.3 62.5 + - - +
135B LEU* 3.3 5.2 + - - +
136B GLY* 3.1 19.9 + - - +
170B ASN 4.2 1.9 - - - +
171B HIS* 2.5 43.3 + - + +
172B PRO* 5.3 0.5 - - - +
173B ARG* 3.1 41.2 + - - +
174B LEU* 4.1 13.4 - - + +
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Residues in contact with THR 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 GLN* 3.1 32.0 + - - +
130B ASP* 4.0 5.8 - - - -
132B ASP* 1.3 76.3 - - - +
134B TYR* 1.3 64.1 + - - +
136B GLY* 3.2 13.9 + - - +
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Residues in contact with TYR 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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47A PRO* 5.2 8.7 - - + -
48A PHE* 3.8 26.7 - + + -
62A HIS* 5.3 5.6 - + - -
87B HIS* 3.6 37.2 + + - +
91B ILE* 3.6 30.3 - - + +
130B ASP 3.1 19.6 + - - +
131B LEU* 3.6 4.3 - - - +
132B ASP 3.3 0.2 - - - -
133B THR* 1.3 77.9 - - - +
135B LEU* 1.3 62.7 + - - +
136B GLY 3.5 0.2 + - - -
138B ARG* 2.9 27.9 + - - -
141B LEU* 3.3 36.9 + - + -
142B ILE* 4.0 2.4 - - - +
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Residues in contact with LEU 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 LEU 2.9 17.2 + - - +
132B ASP* 3.7 5.2 - - - +
134B TYR* 1.3 79.3 - - - +
136B GLY* 1.3 67.6 + - - +
138B ARG* 3.1 56.9 + - - +
139B GLU 4.7 1.1 - - - +
140B TRP* 3.7 28.9 - - - +
141B LEU* 3.9 12.6 - - + +
173B ARG* 3.7 37.9 - - + +
174B LEU* 4.3 13.5 - - + -
177B LEU* 4.2 17.3 - - + -
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Residues in contact with GLY 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 ASP 3.1 11.6 + - - -
133B THR* 3.2 12.1 + - - -
134B TYR 4.5 0.4 - - - -
135B LEU* 1.3 81.2 - - - +
137B GLY* 1.3 59.5 + - - -
138B ARG* 5.3 0.7 - - - -
173B ARG* 3.2 29.2 + - - -
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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