Contacts of the helix formed by residues 151 - 162 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A PRO* 4.1 16.8 - - + -
15B TRP* 4.1 11.2 - + - -
21B SER* 2.7 20.7 + - - -
55B VAL* 4.1 15.6 - - + +
64B GLU* 2.5 33.7 + - - +
66B TYR* 3.5 49.8 - + + +
118B ILE* 4.6 1.3 - - + -
122B LEU* 3.6 27.8 - - + -
141B HIS* 5.3 1.5 - + + +
149B LEU 3.3 1.0 - - - -
150B SER* 1.3 83.0 - - - +
152B LEU* 1.3 60.0 + - - +
153B PRO* 3.3 3.8 - - - -
154B LEU* 3.1 21.1 + - + +
155B MET* 2.8 44.7 + - + +
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Residues in contact with LEU 152 (chain B).
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* 3.9 20.1 - - + +
153A PRO* 3.8 36.6 - - + -
156A LEU* 4.0 14.2 - - + +
141B HIS* 5.5 0.4 - - - +
146B ALA 5.4 1.8 - - - +
149B LEU* 3.3 36.1 - - + +
150B SER 3.4 0.6 - - - -
151B TYR* 1.3 76.5 - - - +
153B PRO* 1.3 72.1 - - + +
155B MET* 3.6 19.3 - - - +
156B LEU* 2.9 25.9 + - - +
170B THR* 3.5 24.9 - - + -
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Residues in contact with PRO 153 (chain B).
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* 5.4 3.8 - - + -
149A LEU* 4.3 7.9 - - + -
152A LEU* 3.8 22.2 - - + -
170A THR* 4.0 7.9 - - - +
177A VAL* 4.1 10.5 - - + -
178A PRO 3.6 11.2 - - - +
179A GLY* 4.0 9.1 - - - +
180A SER* 3.5 26.2 - - - +
149B LEU 5.0 0.7 - - - +
150B SER 3.9 10.8 - - - +
151B TYR* 3.5 4.0 - - - -
152B LEU* 1.3 92.4 - - + +
154B LEU* 1.3 61.7 + - - +
156B LEU* 3.4 8.4 + - + +
157B GLU* 3.0 21.3 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PRO* 3.4 25.1 + - + +
179A GLY* 4.1 8.5 - - - +
55B VAL* 5.3 1.1 - - + -
122B LEU* 4.3 15.9 - - + -
126B GLN* 3.8 37.7 - - + +
151B TYR* 3.1 31.4 + - + +
153B PRO* 1.3 79.6 - - - +
155B MET* 1.3 57.6 + - + +
157B GLU* 3.0 24.5 + - - +
158B LEU* 2.8 48.8 + - + +
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Residues in contact with MET 155 (chain B).
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* 4.2 1.1 - - + -
118B ILE* 3.4 40.4 - - + -
122B LEU* 4.1 11.4 - - + -
139B LEU* 4.1 10.3 - - + -
141B HIS* 3.8 19.3 - - - +
151B TYR* 2.8 33.0 + - + +
152B LEU* 3.1 26.0 + - + +
154B LEU* 1.3 76.2 - - - +
156B LEU* 1.3 53.8 + - - +
158B LEU* 3.3 6.1 + - - +
159B GLN* 2.7 34.8 + - - +
168B ILE* 3.6 40.6 - - + +
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Residues in contact with LEU 156 (chain B).
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* 3.9 24.0 - - + -
155A MET* 4.3 11.4 - - + +
156A LEU* 3.7 24.8 - - + +
159A GLN* 4.0 31.2 - - + -
168A ILE* 3.8 34.5 - - + +
169A GLN* 5.7 0.2 - - - -
170A THR* 4.8 5.2 - - + +
152B LEU 2.9 15.9 + - - +
153B PRO* 3.6 6.3 - - + +
155B MET* 1.3 73.4 - - - +
157B GLU* 1.3 66.3 + - - +
159B GLN* 3.3 1.9 + - - +
160B GLN* 3.0 40.6 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLN* 5.2 4.9 + - - +
179A GLY* 3.6 26.6 + - - +
153B PRO 3.0 14.2 + - - +
154B LEU* 3.3 27.1 - - + +
156B LEU* 1.3 77.6 - - - +
158B LEU* 1.3 57.4 + - + +
160B GLN* 3.3 15.4 + - - +
161B ARG* 3.0 36.6 + - + +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 4.1 26.2 - - + -
125B LEU* 4.1 28.7 - - + +
126B GLN* 4.3 13.7 - - + -
139B LEU* 5.5 0.7 - - + -
154B LEU* 2.8 35.2 + - + +
155B MET* 3.6 8.5 - - + +
157B GLU* 1.3 74.7 - - + +
159B GLN* 1.3 68.1 + - - +
161B ARG* 3.1 38.0 + - - +
162B TYR* 3.0 31.8 + - + +
166B LEU* 3.8 15.3 - - + -
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Residues in contact with GLN 159 (chain B).
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* 3.0 36.5 + - + +
159A GLN* 2.7 33.1 + - - +
160A GLN* 3.7 17.1 - - + +
155B MET 2.7 21.5 + - - +
156B LEU* 3.7 5.1 - - - +
158B LEU* 1.3 76.4 - - - +
160B GLN* 1.3 63.5 + - - +
162B TYR* 3.6 7.4 + - - +
163B GLU* 3.7 6.4 + - - -
164B GLY* 4.3 6.8 + - - +
166B LEU* 3.5 26.0 - - - +
168B ILE* 3.2 38.0 + - + +
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Residues in contact with GLN 160 (chain B).
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* 3.6 32.9 - - + +
166A LEU 4.1 1.4 - - - +
167A ARG* 3.2 15.1 - - - +
168A ILE 2.8 46.7 + - - +
156B LEU* 3.0 33.1 + - + +
157B GLU* 3.6 11.1 - - - +
159B GLN* 1.3 77.2 - - - +
161B ARG* 1.3 63.0 + - - +
163B GLU* 3.2 18.2 + - - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU 2.8 27.8 + - - -
126B GLN* 3.0 24.5 + - - +
127B TYR 4.9 0.4 + - - -
128B GLY* 4.1 6.7 - - - -
157B GLU* 3.0 24.2 + - + +
158B LEU* 3.1 31.3 + - - +
160B GLN* 1.3 77.6 - - - +
162B TYR* 1.3 71.7 + - + +
163B GLU* 3.1 18.6 + - - +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 2.7 47.7 + - + +
128B GLY* 3.4 17.5 - - - -
131B VAL* 4.0 16.5 - - + +
137B LEU* 3.7 27.4 - - + -
158B LEU* 3.0 32.8 + - + +
159B GLN 4.2 1.6 - - - +
160B GLN 3.3 0.4 - - - -
161B ARG* 1.3 91.9 - - + +
163B GLU* 1.3 69.1 + - - +
164B GLY 3.1 1.6 - - - -
165B LYS* 3.0 31.8 + - + +
166B LEU* 3.5 28.9 - - + +
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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