Contacts of the helix formed by residues 136 - 150 (chain C) in PDB entry 4F2N
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 SER 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C ALA* 3.4 18.3 + - - +
134C PHE* 3.2 5.8 + - - +
135C GLY* 1.3 81.0 - - - +
137C VAL* 1.3 63.3 + - - +
138C ASP* 3.5 7.2 + - - +
139C ASP* 2.6 33.9 + - - -
140C PHE* 3.0 22.0 + - - +
23F TYR* 3.9 17.3 - - - -
24F HIS 4.9 1.2 + - - -
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET* 4.0 26.7 - - + -
127C GLU* 3.8 41.3 - - + +
130C ILE* 4.1 14.8 - - + -
131C ALA* 4.1 4.7 - - + +
136C SER* 1.3 73.2 - - - +
138C ASP* 1.3 62.3 + - - +
140C PHE* 3.2 5.1 + - + +
141C MET* 2.9 44.8 + - + +
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Residues in contact with ASP 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER* 3.4 5.4 + - - +
137C VAL* 1.3 79.5 - - - +
139C ASP* 1.3 62.1 + - - +
141C MET* 3.3 17.3 + - - +
142C VAL* 3.1 29.9 + - + +
27F PRO* 3.9 17.8 - - + +
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.4 19.7 - - - +
136C SER* 2.6 25.9 + - - +
138C ASP* 1.3 75.6 - - - +
140C PHE* 1.3 65.6 + - - +
142C VAL* 3.4 1.9 + - - +
143C SER* 3.0 29.1 + - - +
22F CYS 3.4 11.1 - - - +
23F TYR* 3.4 5.2 - - - -
24F HIS* 2.7 49.4 + - - +
27F PRO* 3.4 19.4 - - - +
30F ARG* 5.2 3.1 + - - -
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Residues in contact with PHE 140 (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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130C ILE* 3.5 33.0 - - + -
134C PHE* 3.8 30.4 - + + +
136C SER 3.0 7.6 + - - +
137C VAL* 3.4 7.6 - - + +
139C ASP* 1.3 77.0 - - - +
141C MET* 1.3 67.2 + - + +
143C SER* 3.2 4.5 + - - -
144C PHE* 2.8 49.3 + + + +
159C LEU* 3.9 34.8 - - + -
170C ILE* 3.8 24.0 - - + -
188C PHE* 5.2 1.6 - + - -
213C TRP* 3.6 26.5 - + - -
218C TRP* 4.2 13.5 - + - -
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Residues in contact with MET 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET* 4.7 2.0 - - + -
137C VAL* 2.9 35.6 + - + +
138C ASP* 3.7 16.8 - - - +
139C ASP 3.2 0.2 - - - -
140C PHE* 1.3 87.5 - - + +
142C VAL* 1.3 64.3 + - + +
144C PHE 3.3 0.2 + - - -
145C GLN* 3.0 32.6 + - - +
213C TRP* 3.6 52.1 - - + +
218C TRP* 3.9 29.4 - - + +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASP* 3.1 18.0 + - + +
139C ASP 4.0 3.4 - - - +
141C MET* 1.3 75.9 - - + +
143C SER* 1.3 57.0 + - - +
145C GLN* 3.4 17.3 + - - +
146C GLN* 2.9 44.5 + - + +
27F PRO* 3.4 35.2 - - + +
28F HIS* 3.9 21.5 - - + +
30F ARG* 3.5 22.2 - - - +
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 5.2 4.6 - - - +
139C ASP* 3.0 19.5 + - - +
140C PHE* 3.5 6.1 - - - -
142C VAL* 1.3 78.4 - - - +
144C PHE* 1.3 60.5 + - - +
146C GLN* 3.4 6.8 + - - +
147C ALA* 3.0 23.9 + - - +
170C ILE* 3.8 16.1 - - - +
21F LEU* 5.2 9.6 - - - +
30F ARG* 4.8 8.9 + - - +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PHE* 2.8 38.7 + + + +
141C MET 3.7 4.5 - - - +
143C SER* 1.3 76.1 - - - +
145C GLN* 1.3 65.3 + - + +
147C ALA* 3.2 6.4 + - - +
148C GLY* 2.9 19.8 + - - -
157C THR* 3.3 43.4 - - + +
158C TRP 3.8 11.0 - - - -
159C LEU* 4.0 0.4 - - + -
170C ILE* 3.6 14.9 - - + +
188C PHE* 3.5 33.9 - + - -
190C ALA* 3.6 22.0 - - + -
209C LEU* 4.5 10.8 - - + -
212C LEU* 5.2 1.6 - - + -
213C TRP* 3.5 23.6 - + + -
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Residues in contact with GLN 145 (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 MET* 3.0 24.9 + - - +
142C VAL* 3.5 15.3 + - + +
144C PHE* 1.3 79.5 - - + +
146C GLN* 1.3 59.1 + - + +
148C GLY* 3.2 2.1 + - - -
149C VAL* 2.9 37.1 + - + +
206C ALA 5.0 2.0 + - - +
209C LEU* 3.6 26.6 - - + +
210C LYS* 3.9 22.7 - - - +
213C TRP* 2.8 35.7 + - + +
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Residues in contact with GLN 146 (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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142C VAL* 2.9 31.9 + - + +
143C SER* 3.8 7.0 - - - +
145C GLN* 1.3 74.0 - - + +
147C ALA* 1.3 66.6 + - - +
149C VAL* 3.4 8.9 + - - +
150C ASN* 3.0 42.7 + - - +
30F ARG* 3.9 31.0 - - - +
79F GLY* 4.6 12.1 - - - +
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Residues in contact with ALA 147 (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 SER 3.0 14.8 + - - +
144C PHE 3.6 7.0 - - - +
146C GLN* 1.3 75.6 - - - +
148C GLY* 1.3 61.9 + - - +
150C ASN* 3.4 5.0 + - - +
151C ASN* 3.1 24.6 + - - +
157C THR* 3.9 8.5 - - + -
170C ILE* 3.8 24.5 - - + -
172C SER* 3.8 9.8 + - - +
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Residues in contact with GLY 148 (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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144C PHE 2.9 13.2 + - - -
145C GLN 3.2 3.8 + - - -
147C ALA* 1.3 78.0 - - - +
149C VAL* 1.3 57.8 + - - +
151C ASN* 3.4 6.8 + - - +
157C THR* 3.4 20.1 + - - -
192C VAL* 4.1 5.4 - - - +
205C ARG* 2.9 26.7 + - - -
209C LEU* 3.7 17.5 - - - -
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Residues in contact with VAL 149 (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 GLN* 2.9 26.0 + - + +
146C GLN* 3.4 8.9 + - - +
148C GLY* 1.3 73.8 - - - +
150C ASN* 1.3 71.2 + - - +
151C ASN 3.3 1.3 + - - +
152C PHE* 5.7 0.2 - - - -
205C ARG* 3.7 18.8 + - + +
206C ALA* 3.7 39.5 - - + +
209C LEU* 4.0 6.3 - - + -
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Residues in contact with ASN 150 (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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146C GLN* 3.0 34.1 + - - +
147C ALA* 3.7 5.4 - - - +
149C VAL* 1.3 84.6 - - - +
151C ASN* 1.3 58.9 + - - +
152C PHE* 3.0 12.4 + - - +
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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