Contacts of the helix formed by residues 151 - 164 (chain C) in PDB entry 4IYM
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 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.4 2.6 - - - +
99C ASP* 3.2 10.2 + - - -
100C ILE* 5.2 1.8 - - - -
149C PHE 3.2 0.4 - - - -
150C PRO* 1.3 82.4 - - - +
152C MSE 1.3 66.1 + - - +
153C ILE 3.4 0.2 + - - -
154C PRO* 3.6 3.1 - - - +
155C MSE 3.2 42.4 + - - +
179C VAL* 3.8 16.7 - - - +
183C LEU* 4.1 1.9 - - - +
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Residues in contact with MSE 152 (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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99C ASP* 2.6 31.5 + - - +
102C ARG* 3.3 58.8 - - + +
103C GLY* 3.9 8.4 - - - +
149C PHE* 3.6 38.1 + - + -
151C GLY* 1.3 74.7 - - - +
153C ILE* 1.3 68.8 + - + +
155C MSE 3.3 3.1 + - - +
156C TRP* 2.9 66.7 + - + +
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Residues in contact with ILE 153 (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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145C THR* 3.5 22.4 - - + -
146C PRO* 3.7 17.9 - - + -
148C ASN* 4.3 3.8 - - - +
149C PHE* 3.2 31.9 + - + +
152C MSE 1.3 88.4 - - + +
154C PRO* 1.3 70.5 - - + +
156C TRP* 3.1 32.3 + - + +
157C MSE 3.4 11.7 + - + +
222C VAL* 3.7 40.6 - - + -
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Residues in contact with PRO 154 (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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145C THR* 3.8 28.0 - - + +
149C PHE 3.4 13.9 - - - +
150C PRO* 3.3 20.6 - - + +
151C GLY 3.6 8.7 - - - +
153C ILE* 1.3 90.1 - - + +
155C MSE 1.3 51.1 + - - +
157C MSE 3.2 4.5 + - + +
158C PHE* 2.8 46.4 + - + +
168C PHE* 4.9 1.0 - - - -
170C LEU* 3.7 30.7 - - + -
180C PRO* 4.7 3.6 - - + -
183C LEU* 4.7 4.7 - - + -
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Residues in contact with MSE 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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70C PHE* 4.0 12.6 - - - -
74C LEU* 3.8 17.9 - - - -
100C ILE* 3.7 23.1 - - + +
103C GLY* 3.5 40.4 - - - +
104C LEU 3.8 2.2 - - - -
106C VAL* 3.9 3.5 - - - +
107C CYS* 4.0 5.6 - - - -
151C GLY* 3.2 38.9 + - - +
152C MSE 3.3 4.4 + - - +
153C ILE 3.2 0.8 - - - -
154C PRO* 1.3 74.1 - - - +
156C TRP* 1.3 68.5 + - - +
157C MSE 3.0 2.5 + - - -
158C PHE* 3.7 28.0 - - + -
159C ALA* 3.1 26.3 + - - +
183C LEU* 4.0 16.8 - - + -
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Residues in contact with TRP 156 (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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102C ARG* 4.7 8.9 + - - +
106C VAL* 3.6 30.6 - - + +
152C MSE 2.9 61.8 + - + +
153C ILE* 3.1 33.7 - - + +
155C MSE 1.3 73.6 - - - +
157C MSE 1.3 62.5 + - + +
160C PRO* 3.1 25.3 - - - +
222C VAL* 4.3 22.4 - - + -
245C PHE* 6.0 3.8 - + + -
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Residues in contact with MSE 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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143C GLY* 3.6 26.5 - - - -
144C ILE 3.6 20.9 - - - +
145C THR* 3.7 23.6 - - + -
153C ILE* 3.8 7.0 - - + +
154C PRO* 3.2 5.7 + - - +
155C MSE 3.0 0.2 - - - -
156C TRP* 1.3 84.0 - - + +
158C PHE* 1.3 66.6 + - - +
159C ALA 3.3 0.6 + - - -
160C PRO* 3.6 5.4 - - - +
161C ALA* 3.3 22.9 + - - +
168C PHE* 3.7 15.8 - - + -
220C SER* 3.5 33.7 - - - +
222C VAL* 3.6 31.0 - - + +
243C GLN* 5.2 2.7 - - - +
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Residues in contact with PHE 158 (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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67C PHE* 4.3 6.7 - + - -
70C PHE* 4.1 20.2 - + - -
107C CYS* 5.0 0.2 - - - -
154C PRO* 2.8 32.5 + - + +
155C MSE 3.7 30.3 - - + -
157C MSE 1.3 71.4 - - - +
159C ALA* 1.3 65.0 + - + +
162C ILE* 3.0 41.2 + - + +
168C PHE* 3.5 32.8 - - + -
170C LEU* 5.2 5.4 - - + -
183C LEU* 4.5 14.6 - - + -
187C MSE 4.0 23.6 - - + -
197C LEU* 3.9 31.2 - - + -
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Residues in contact with ALA 159 (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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67C PHE* 3.3 26.2 - - + -
106C VAL* 4.0 9.9 - - + -
107C CYS* 4.2 14.6 - - - +
110C VAL* 3.9 13.0 - - + -
155C MSE 3.1 16.2 + - - +
158C PHE* 1.3 80.1 - - + +
160C PRO* 1.3 66.8 - - + +
163C ALA* 2.9 30.8 + - - +
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Residues in contact with PRO 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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106C VAL* 3.9 9.9 - - + -
109C PHE* 6.2 2.2 - - + -
110C VAL* 3.7 17.0 - - + -
113C ILE* 6.0 0.4 - - + -
156C TRP 3.1 27.8 - - - +
157C MSE 3.6 6.1 - - - +
159C ALA* 1.3 89.6 - - + +
161C ALA* 1.3 65.0 + - - +
163C ALA* 4.3 1.6 - - + -
164C CYS* 3.0 35.4 + - - -
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Residues in contact with ALA 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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141C GLY* 5.9 1.6 - - - -
157C MSE 3.3 18.2 + - - +
158C PHE 4.0 1.1 - - - +
160C PRO* 1.3 79.8 - - - +
162C ILE* 1.3 61.4 + - - +
164C CYS* 3.5 1.8 + - - -
166C ASN* 2.8 45.0 + - + +
168C PHE* 3.6 29.8 - - + -
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Residues in contact with ILE 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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55C TRP* 2.9 36.9 + - + +
67C PHE* 3.9 13.7 - - + -
158C PHE* 3.0 40.2 + - + +
161C ALA* 1.3 73.1 - - - +
163C ALA* 1.3 66.6 + - - +
164C CYS 3.1 1.8 - - - -
165C GLY 3.0 5.5 + - - -
166C ASN 3.6 7.4 - - - +
168C PHE* 4.0 14.1 - - + -
187C MSE 4.2 5.6 - - + -
192C LEU* 3.7 26.9 - - + -
196C ILE* 3.8 15.5 - - + +
197C LEU* 3.7 30.3 - - + -
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Residues in contact with ALA 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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63C ARG* 2.9 32.1 + - + +
67C PHE* 3.7 15.8 - - + -
110C VAL* 3.6 25.8 - - + +
113C ILE* 3.4 28.6 - - + +
159C ALA 2.9 20.8 + - - +
160C PRO 4.0 2.9 - - - +
162C ILE* 1.3 76.2 - - - +
164C CYS* 1.3 57.4 + - - +
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Residues in contact with CYS 164 (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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63C ARG* 3.9 4.1 + - - -
113C ILE* 4.0 18.4 - - - -
117C GLN* 3.0 34.9 + - - +
137C PRO* 3.7 15.8 - - + +
160C PRO* 3.0 28.9 + - - +
161C ALA* 4.7 0.4 - - - -
162C ILE 3.1 0.4 - - - -
163C ALA* 1.3 76.4 - - - +
165C GLY* 1.3 57.3 + - - +
166C ASN* 3.6 17.5 - - - +
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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