Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 3FPK
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 TYR 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.3 6.3 - + - -
21A SER* 2.7 20.2 + - - -
55A VAL* 4.1 15.1 - - + +
64A GLU* 2.6 33.8 + - - +
66A TYR* 3.5 49.4 - + + +
118A ILE* 4.4 2.7 - - + -
122A LEU* 3.5 28.9 - - + -
141A HIS* 5.3 2.7 - + + -
149A LEU 3.3 1.2 - - - -
150A SER* 1.3 85.7 - - - +
152A LEU* 1.3 58.6 + - - +
153A PRO* 3.4 3.6 - - - -
154A LEU* 3.1 22.4 + - + +
155A MET* 2.8 41.4 + - + +
178B PRO* 4.2 15.5 - - + -
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Residues in contact with LEU 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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146A ALA 5.1 2.5 - - - +
149A LEU* 3.6 34.3 - - + +
150A SER 3.4 1.0 - - - -
151A TYR* 1.3 77.2 - - - +
153A PRO* 1.4 71.5 - - + +
155A MET* 3.1 12.3 + - - +
156A LEU* 2.9 26.6 + - + +
170A THR* 3.8 23.6 - - + -
152B LEU* 3.9 19.7 - - + +
153B PRO* 3.8 38.4 - - + -
156B LEU* 3.9 22.9 - - + -
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Residues in contact with PRO 153 (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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149A LEU 5.2 0.4 - - - +
150A SER 4.2 9.6 - - - +
151A TYR* 3.6 3.6 - - - -
152A LEU* 1.4 91.6 - - + +
154A LEU* 1.3 61.0 + - - +
156A LEU* 3.3 15.9 + - + +
157A GLU* 3.1 19.2 + - - +
146B ALA* 5.6 2.0 - - + -
149B LEU* 4.8 4.9 - - + -
152B LEU* 3.8 18.2 - - + -
170B THR* 4.1 5.2 - - - +
177B VAL* 4.1 12.6 - - + -
178B PRO 3.4 16.2 - - - +
179B GLY* 3.8 13.3 - - - +
180B SER* 3.6 23.8 - - - +
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Residues in contact with LEU 154 (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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55A VAL* 5.2 1.6 - - + -
122A LEU* 4.3 14.6 - - + -
126A GLN* 3.7 42.6 - - + +
151A TYR* 3.1 37.2 + - + +
153A PRO* 1.3 79.1 - - - +
155A MET* 1.3 58.2 + - + +
157A GLU* 3.1 24.8 + - + +
158A LEU* 2.9 40.4 + - + +
178B PRO* 3.5 22.5 + - + +
179B GLY* 4.4 1.8 - - - +
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Residues in contact with MET 155 (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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118A ILE* 3.9 26.0 - - + -
122A LEU* 4.7 8.5 - - + -
139A LEU* 4.0 13.9 - - + -
141A HIS* 3.8 30.1 - - + +
151A TYR* 2.8 26.5 + - + +
152A LEU* 3.1 28.9 + - - +
154A LEU* 1.3 74.7 - - - +
156A LEU* 1.3 59.5 + - - +
158A LEU* 3.8 5.1 - - + +
159A GLN* 2.8 26.9 + - - +
168A ILE* 3.3 41.0 - - + +
170A THR* 4.8 5.2 - - - -
156B LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 156 (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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152A LEU* 2.9 21.6 + - + +
153A PRO* 3.5 13.7 - - + +
155A MET* 1.3 72.9 - - - +
157A GLU* 1.3 63.1 + - - +
160A GLN* 3.2 10.0 + - - +
152B LEU* 4.0 24.9 - - + +
155B MET* 5.1 0.2 - - + -
156B LEU* 3.7 39.0 - - + +
159B GLN* 3.0 45.2 + - - +
168B ILE* 3.8 37.0 - - + +
170B THR* 4.6 4.5 - - + -
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Residues in contact with GLU 157 (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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153A PRO 3.1 8.6 + - - +
154A LEU* 3.1 22.9 + - + +
156A LEU* 1.3 79.4 - - - +
158A LEU* 1.3 65.6 + - + +
160A GLN* 3.3 6.3 + - - +
161A ARG* 3.0 26.9 + - + +
179B GLY* 3.5 26.0 + - - +
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Residues in contact with LEU 158 (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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122A LEU* 4.1 25.8 - - + -
125A LEU* 3.7 44.9 - - + +
126A GLN* 4.0 15.3 - - + -
139A LEU* 5.4 1.8 - - + -
154A LEU* 2.9 32.8 + - + +
155A MET* 3.9 7.4 - - + +
157A GLU* 1.3 74.4 - - + +
159A GLN* 1.3 69.2 + - - +
161A ARG* 3.2 16.9 + - - +
162A TYR* 3.0 36.9 + - + +
166A LEU* 3.8 15.9 - - + -
168A ILE* 4.9 0.7 - - + -
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Residues in contact with GLN 159 (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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155A MET 2.8 17.4 + - - +
156A LEU 3.8 3.8 - - - +
157A GLU 3.3 0.2 - - - -
158A LEU* 1.3 79.0 - - - +
160A GLN* 1.3 65.7 + - - +
162A TYR* 3.4 2.3 + - - +
163A GLU* 3.2 16.6 + - - -
164A GLY* 4.0 19.4 + - - -
166A LEU* 3.8 23.3 - - - +
168A ILE* 4.1 4.7 - - + -
156B LEU* 4.0 11.0 - - + -
159B GLN* 2.7 44.0 + - - +
160B GLN* 3.6 41.9 - - + +
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Residues in contact with GLN 160 (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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156A LEU 3.2 13.7 + - - +
157A GLU* 3.8 5.6 - - - +
159A GLN* 1.3 85.0 - - - +
161A ARG* 1.3 65.1 + - - +
163A GLU* 3.1 22.0 + - - +
159B GLN* 3.9 13.2 - - + +
164B GLY* 6.3 3.4 - - - -
166B LEU 4.8 0.9 - - - +
167B ARG* 3.5 46.3 - - - +
168B ILE 4.8 1.7 + - - +
198B VAL 4.6 4.4 + - - -
249B MG 4.4 15.4 - - - -
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Residues in contact with ARG 161 (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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125A LEU 3.5 14.0 + - - -
126A GLN* 2.7 40.3 + - - +
127A TYR 3.6 11.9 + - - -
128A GLY* 3.6 8.3 - - - -
157A GLU* 3.0 18.6 + - + +
158A LEU* 3.2 19.0 + - - +
160A GLN* 1.3 79.4 - - - +
162A TYR* 1.3 76.1 + - + +
163A GLU* 3.5 10.7 + - - +
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Residues in contact with TYR 162 (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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125A LEU* 2.7 41.6 + - + +
128A GLY* 3.3 19.8 - - - -
131A VAL* 4.1 14.9 - - + +
137A LEU* 3.7 28.3 - - + -
158A LEU* 3.0 32.6 + - + +
159A GLN 4.2 1.1 - - - +
161A ARG* 1.3 94.6 + - + +
163A GLU* 1.3 70.3 + - - +
164A GLY 3.3 1.1 - - - -
165A LYS* 3.0 27.3 + - + +
166A LEU* 3.5 34.8 - - + +
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Residues in contact with GLU 163 (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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159A GLN 3.2 4.1 + - - -
160A GLN 3.1 19.4 + - - +
161A ARG 3.9 8.3 - - - +
162A TYR* 1.3 81.1 - - - +
164A GLY* 1.3 58.7 + - - +
165A LYS* 3.5 0.7 + - - +
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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