Contacts of the helix formed by residues 154 - 163 (chain C) in PDB entry 1IR1
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 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C PRO* 4.0 3.7 - - - +
153C HIS* 1.3 74.7 - - - +
155C ILE* 1.3 66.9 + - - -
156C GLN 3.4 2.5 + - - -
157C VAL 3.4 0.5 + - - -
158C GLU* 2.9 27.9 + - - +
324C ASP* 2.8 20.5 + - - -
372C PRO* 3.8 11.0 - - - -
373C GLY 3.3 15.7 - - - -
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Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C GLY* 1.3 71.3 - - - +
156C GLN* 1.3 64.9 + - - +
158C GLU* 3.8 3.8 - - - +
159C ARG* 3.1 31.2 + - + +
324C ASP 5.4 0.4 + - - -
350C ARG* 3.9 28.5 - - + +
373C GLY* 3.2 25.9 + - - +
374C VAL* 3.7 17.9 - - - +
375C LEU* 3.8 31.8 - - + +
397C ASP* 3.9 19.3 - - + +
108U ARG* 3.8 24.5 - - - +
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Residues in contact with GLN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C GLY 3.5 0.6 - - - -
155C ILE* 1.3 79.8 - - - +
157C VAL* 1.3 79.5 + - + +
159C ARG* 3.3 3.9 + - - +
160C ASP* 3.1 35.8 + - - +
181D SER* 3.6 28.4 - - - -
182D ALA 5.1 1.2 + - - -
211D PHE 4.4 8.9 + - - +
108U ARG* 3.3 13.3 + - - +
109U GLN* 3.0 34.0 + - - +
110U VAL* 3.6 22.4 - - + +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C HIS* 3.7 39.2 + - + +
154C GLY 3.4 1.8 + - - -
156C GLN* 1.3 90.7 - - + +
158C GLU* 1.3 57.4 + - - +
160C ASP* 3.3 7.9 + - - +
161C LYS* 2.9 38.4 + - + +
182D ALA* 5.7 4.9 - - + -
216D ASP* 3.5 39.3 - - + +
220D PHE* 5.3 2.9 - - + -
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Residues in contact with GLU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C HIS* 4.7 0.2 - - - +
154C GLY 2.9 19.4 + - - +
155C ILE* 3.8 4.5 - - - +
157C VAL* 1.3 77.7 - - - +
159C ARG* 1.3 64.6 + - + +
161C LYS* 3.2 3.0 + - - +
162C LEU* 3.0 30.6 + - + +
169C LEU* 4.2 3.9 - - + +
199C PHE* 4.0 14.2 - - - -
290C LEU* 3.9 35.5 - - + +
324C ASP* 3.8 14.2 - - - +
325C HIS* 2.5 43.5 + - - -
375C LEU* 3.7 16.7 - - + +
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Residues in contact with ARG 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE* 3.1 23.0 + - + +
156C GLN* 3.7 4.3 - - - +
158C GLU* 1.3 80.5 - - + +
160C ASP* 1.3 58.3 + - - +
162C LEU* 5.0 2.0 - - - -
163C ASN* 2.8 26.0 + - - -
164C LYS* 2.9 46.4 + - + +
165C TYR* 3.5 28.7 - - + +
166C GLY 4.7 3.1 - - - +
167C ARG 3.1 18.4 + - - -
168C PRO* 4.7 0.2 - - - +
169C LEU* 4.4 20.1 - - + +
375C LEU* 5.3 6.7 - - + +
396C ASP* 3.0 32.7 + - - +
397C ASP* 3.0 26.3 + - - +
398C SER 4.8 0.8 - - - +
110U VAL* 4.3 17.6 - - + +
111U GLN 5.0 0.4 - - - -
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Residues in contact with ASP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLN* 3.1 38.5 + - - +
157C VAL* 3.6 7.3 - - - +
158C GLU 3.2 0.2 - - - -
159C ARG* 1.3 76.3 - - - +
161C LYS* 1.3 64.1 + - - +
163C ASN* 3.6 5.7 + - - -
165C TYR* 2.6 34.4 + - - -
181D SER* 4.7 3.6 + - - -
183D LYS* 3.3 34.7 + - + +
220D PHE* 3.6 29.1 - - + -
65U ARG* 4.2 4.2 - - - -
109U GLN 5.0 1.8 - - - +
110U VAL* 5.7 2.3 - - - -
111U GLN* 5.4 3.1 + - - +
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Residues in contact with LYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C HIS* 3.8 19.2 + - - -
157C VAL* 2.9 25.2 + - + +
158C GLU* 3.2 6.7 + - - +
160C ASP* 1.3 76.8 - - - +
162C LEU* 1.3 69.3 + - + +
235C ILE* 4.0 5.4 - - - +
288C GLY* 4.8 10.5 + - - -
290C LEU* 5.5 8.7 - - + +
215D ARG* 5.7 0.6 - - - +
216D ASP* 2.9 29.6 + - - +
219D LEU* 4.1 21.1 - - + +
220D PHE* 3.9 25.1 - - + -
60U GLY* 3.8 25.7 - - - +
62U TYR* 4.0 4.7 - - - -
65U ARG* 2.9 28.4 + - - +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLU* 3.0 31.5 + - + +
159C ARG* 4.4 1.6 - - - +
161C LYS* 1.3 80.4 - - + +
163C ASN* 1.3 71.1 + - - +
164C LYS* 3.4 29.4 + - + +
169C LEU* 4.8 3.6 - - + -
199C PHE* 3.6 35.7 - - + -
235C ILE* 3.5 38.6 - - + +
236C LYS 6.1 0.2 - - - -
263C PRO* 4.4 17.3 - - + -
290C LEU* 4.1 18.4 - - + -
13U GLU* 4.8 0.9 - - - +
60U GLY* 6.5 0.4 - - - -
62U TYR* 5.1 2.5 - - + -
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Residues in contact with ASN 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ARG 2.8 12.5 + - - -
160C ASP 3.6 2.6 + - - -
161C LYS 3.3 2.8 - - - -
162C LEU* 1.3 80.4 - - - +
164C LYS* 1.3 58.7 + - - +
165C TYR* 3.7 16.2 + - - -
235C ILE* 4.5 4.3 - - + -
183D LYS* 3.3 23.0 + - - -
13U GLU* 3.9 17.9 - - - +
51U VAL* 5.1 6.2 - - + +
64U GLY 5.2 0.6 + - - -
65U ARG* 4.1 35.8 + - + +
100U ARG* 4.0 25.3 + - - +
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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