Contacts of the helix formed by residues 140 - 152 (chain A) in PDB entry 4IRQ
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLN* 2.8 10.8 + - - -
138A ARG 3.2 0.4 + - - -
139A PHE* 1.3 71.8 - - - +
141A ARG* 1.3 60.1 - - - +
142A ALA* 3.5 6.4 + - - +
143A ALA* 2.9 33.5 + - - +
144A LEU* 3.1 25.6 + - - +
219A ASN 3.1 27.3 + - - +
221A PHE 3.1 21.6 + - - +
222A TRP* 3.4 34.2 - - + -
314A LEU* 3.8 14.1 - - + -
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Residues in contact with ARG 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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100A PRO* 3.9 19.0 - - + +
139A PHE* 3.7 23.4 + - + -
140A ASN* 1.3 72.9 - - - +
142A ALA* 1.3 62.9 + - - +
144A LEU* 3.3 4.6 + - - +
145A ILE* 3.1 30.4 + - + +
161A MET* 4.2 24.5 + - - +
163A ASP* 2.9 29.6 + - - +
200A VAL 5.2 0.8 + - - -
201A GLY* 4.2 2.6 - - - -
202A GLY 3.4 31.3 + - - +
217A MET* 4.2 14.6 - - - +
221A PHE 4.9 1.0 + - - -
227A GLU* 2.9 37.3 + - + +
228A ASP* 4.5 5.9 - - - +
402A UDP 4.2 7.2 - - - -
403A TRS 3.8 20.2 + - - +
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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
----------------------------------------------------------
140A ASN* 3.3 4.6 + - - +
141A ARG* 1.3 77.1 - - - +
143A ALA* 1.3 66.7 + - - +
145A ILE* 3.3 4.3 + - - +
146A ASN* 3.0 24.3 + - - +
217A MET* 3.7 26.9 - - + +
218A SER 3.2 24.0 - - - +
221A PHE* 5.4 1.1 - - + -
227A GLU* 3.7 31.0 - - + +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ASN* 2.9 33.6 + - - +
142A ALA* 1.3 77.1 - - - +
144A LEU* 1.3 61.4 + - - +
146A ASN* 3.4 4.7 - - - +
147A VAL* 3.1 25.9 + - - +
218A SER 4.0 1.0 + - - -
219A ASN* 3.7 26.9 - - + +
222A TRP* 5.7 0.9 - - + -
290A VAL* 4.1 4.4 - - + +
314A LEU* 3.9 19.1 - - + -
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Residues in contact with LEU 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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100A PRO* 4.4 4.7 - - + -
101A PHE 4.1 1.3 - - - +
131A LEU* 3.5 31.8 - - + +
133A GLN* 3.6 21.8 - - + +
139A PHE* 3.5 37.5 - - + -
140A ASN 3.1 21.8 + - - +
141A ARG* 3.6 4.3 - - - +
142A ALA 3.1 0.4 - - - -
143A ALA* 1.3 75.7 - - - +
145A ILE* 1.3 65.5 + - - +
147A VAL* 3.0 6.9 + - - +
148A GLY 2.9 19.6 + - - -
312A ILE* 3.9 31.6 - - + -
314A LEU* 3.9 17.3 - - + -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.8 18.8 - - + +
100A PRO* 3.6 33.9 - - + -
131A LEU* 4.2 8.5 - - + -
141A ARG* 3.1 22.3 + - + +
142A ALA 3.5 6.3 - - - +
144A LEU* 1.3 76.3 - - - +
146A ASN* 1.3 61.6 + - - +
148A GLY* 3.2 1.6 + - - -
149A PHE* 2.9 22.9 + - - +
159A ILE* 4.8 0.7 - - + -
161A MET* 3.8 43.1 - - + -
211A TYR* 3.6 16.6 - - + +
217A MET* 3.9 13.0 - - + -
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Residues in contact with ASN 146 (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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142A ALA 3.0 12.7 + - - +
143A ALA 3.4 10.8 - - - +
145A ILE* 1.3 77.2 - - - +
147A VAL* 1.3 61.4 + - - +
149A PHE* 3.4 5.4 + - - +
150A LEU* 3.2 27.3 + - - +
211A TYR* 2.5 30.5 + - - -
216A GLY* 3.6 3.8 - - - -
217A MET 2.7 38.1 + - - -
218A SER 4.2 0.2 + - - -
219A ASN* 2.9 22.7 + - - +
286A GLY 3.7 8.1 - - - -
287A LEU* 3.8 11.1 - - + +
290A VAL* 4.3 11.0 - - + -
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Residues in contact with VAL 147 (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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143A ALA 3.1 17.8 + - - +
144A LEU* 3.0 9.6 + - - +
146A ASN* 1.3 72.2 - - - +
148A GLY* 1.3 63.0 + - - +
150A LEU* 3.1 6.8 + - - +
151A GLU* 2.8 36.2 + - + +
290A VAL* 4.2 4.7 - - + -
292A TYR* 3.5 50.3 - - + -
294A VAL* 4.9 0.2 - - + -
310A LEU* 5.1 0.4 - - + -
312A ILE* 3.6 29.8 - - + -
314A LEU* 3.9 16.4 - - + -
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Residues in contact with GLY 148 (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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98A LEU* 3.9 9.8 - - - +
129A TYR* 5.5 0.6 - - - -
131A LEU* 3.6 31.3 - - - +
144A LEU 2.9 10.3 + - - -
145A ILE 3.2 3.1 + - - -
147A VAL* 1.3 73.0 - - - +
149A PHE* 1.3 56.3 - - - +
151A GLU* 4.4 3.8 - - - -
152A SER* 2.2 39.4 + - - -
310A LEU* 4.8 0.9 - - - -
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Residues in contact with PHE 149 (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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98A LEU* 3.8 6.3 - - + +
145A ILE 2.9 13.1 + - - +
146A ASN 3.4 9.9 - - - +
147A VAL 3.2 0.2 - - - -
148A GLY* 1.3 75.3 - - - +
150A LEU* 1.3 65.5 + - + +
152A SER* 3.2 14.3 + - - +
159A ILE* 3.9 20.9 - - + -
208A LYS* 3.6 67.6 + - + -
211A TYR* 3.3 41.7 - + + -
212A ARG* 3.7 25.4 - - + -
287A LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 150 (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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146A ASN 3.2 10.9 + - - +
147A VAL 3.1 7.4 + - - +
149A PHE* 1.3 83.0 - - + +
151A GLU* 1.3 62.8 + - - +
152A SER 3.4 4.4 + - - +
287A LEU* 3.7 30.1 - - + +
290A VAL* 3.6 30.1 - - + +
292A TYR* 3.8 24.0 - - + +
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Residues in contact with GLU 151 (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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129A TYR* 4.2 7.4 - - - -
147A VAL* 2.8 30.3 + - + +
148A GLY 3.2 1.5 + - - +
150A LEU* 1.3 78.5 - - - +
152A SER* 1.3 63.6 + - - +
292A TYR* 2.6 29.2 + - - +
294A VAL* 3.7 16.2 - - + +
297A ARG* 3.2 39.1 + - - +
310A LEU* 3.6 22.7 - - + +
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Residues in contact with SER 152 (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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96A ALA* 4.2 6.3 - - - +
98A LEU* 4.1 3.5 - - - +
129A TYR* 3.7 28.9 - - - -
148A GLY 2.2 30.2 + - - -
149A PHE* 3.2 14.4 + - - +
150A LEU 3.4 6.2 - - - +
151A GLU* 1.3 80.0 - - - +
153A SER* 1.3 68.1 + - - +
154A ASN* 3.3 4.3 + - - +
156A THR* 3.8 14.6 + - - -
159A ILE* 5.2 1.7 - - - +
208A LYS* 5.1 3.5 + - - -
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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
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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