Contacts of the helix formed by residues 134 - 141 (chain B) in PDB entry 4FK8
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 LEU 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.0 30.3 - - + -
129B SER* 3.7 19.3 - - - +
131B GLY 3.4 18.4 + - - +
132B THR 3.0 1.0 - - - -
133B GLY* 1.3 76.4 - - - +
135B ALA* 1.3 68.0 + - - +
136B PRO 3.4 0.2 - - - -
137B PHE* 3.0 18.7 + - - +
138B MET* 3.1 47.2 + - + +
155B LEU* 5.3 2.5 - - + -
157B HIS* 4.9 3.8 - - + -
159B CYS* 3.1 35.7 - - - -
164B GLU 5.8 0.2 - - - +
167B TYR* 4.5 6.3 - - + -
168B MET* 4.3 15.3 - - + -
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Residues in contact with ALA 135 (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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69B SER* 3.9 4.9 - - - -
71B VAL* 3.8 26.4 - - + +
82B PHE* 4.3 11.4 - - + -
132B THR 2.8 17.4 + - - +
133B GLY 3.0 0.4 - - - -
134B LEU* 1.3 80.7 - - - +
136B PRO* 1.4 66.1 - - + +
138B MET* 3.0 25.3 + - - +
139B SER 3.8 2.1 + - - -
301B FAD 3.5 22.0 - - - +
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY* 3.7 26.5 - - - +
69B SER* 3.2 28.3 - - - +
70B ILE 4.8 3.6 - - - +
114B LEU* 3.6 26.9 - - + -
132B THR 4.3 0.7 - - - +
133B GLY* 3.2 17.5 - - - +
135B ALA* 1.4 90.5 - - + +
137B PHE* 1.3 59.8 + - + +
139B SER* 3.1 19.9 + - - -
140B ILE* 3.1 16.2 + - + +
234B CYS* 3.7 11.2 - - + -
266B GLU* 4.8 0.2 - - - +
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Residues in contact with PHE 137 (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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114B LEU* 4.5 7.0 - - + -
127B MET* 3.6 28.7 - - + -
128B LEU 3.9 5.4 - - - -
129B SER* 3.7 13.9 - - - -
133B GLY 3.4 24.5 - - - -
134B LEU 3.0 6.1 + - - +
136B PRO* 1.3 73.1 - - + +
138B MET* 1.3 65.7 + - + +
139B SER 3.1 1.8 - - - -
140B ILE* 3.7 18.8 - - + +
141B ILE* 2.9 33.4 + - - +
155B LEU* 3.7 28.9 - - + -
232B MET* 3.6 48.2 - - + -
233B LEU 4.4 0.7 - - - -
234B CYS* 3.7 20.9 - - + -
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Residues in contact with MET 138 (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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71B VAL* 3.5 22.2 - - + -
134B LEU* 3.1 42.7 + - + +
135B ALA* 3.0 12.9 + - - +
137B PHE* 1.3 81.0 - - - +
139B SER* 1.3 57.8 - - - +
141B ILE* 3.7 17.8 - - + +
142B ARG* 2.9 25.6 + - - -
155B LEU* 3.6 31.9 - - + -
167B TYR* 4.6 3.1 - - + -
168B MET* 4.0 21.1 - - - +
171B ILE* 3.7 30.3 - - + +
191B TYR* 4.9 1.6 - - + -
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Residues in contact with SER 139 (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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47B PHE* 4.2 0.3 - - - -
49B ASN* 2.8 42.0 + - - +
50B GLY 3.8 8.7 - - - -
70B ILE 3.4 21.5 + - - -
71B VAL 3.2 9.0 + - - -
72B SER 2.7 22.3 + - - -
73B PRO 4.8 0.2 - - - -
135B ALA 3.8 0.6 + - - -
136B PRO 3.1 11.2 + - - -
137B PHE 3.1 0.2 - - - -
138B MET* 1.3 76.9 - - - +
140B ILE* 1.3 65.5 + - - +
141B ILE 3.3 0.2 - - - -
142B ARG* 3.0 13.3 + - - +
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Residues in contact with ILE 140 (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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49B ASN* 3.5 26.2 - - - +
50B GLY* 3.6 15.9 - - - -
114B LEU* 4.2 12.6 - - + +
127B MET* 3.5 22.2 - - + -
136B PRO* 3.1 11.5 + - + +
137B PHE* 3.3 27.1 + - + +
139B SER* 1.3 75.8 - - - +
141B ILE* 1.3 57.9 + - - +
142B ARG 3.0 0.2 - - - -
143B ASP* 2.9 23.6 + - + +
146B ILE* 3.7 32.0 - - + +
232B MET* 3.9 21.3 - - + -
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Residues in contact with ILE 141 (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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127B MET* 3.7 27.8 - - + -
137B PHE 2.9 25.5 + - - +
138B MET* 3.7 25.1 - - + +
140B ILE* 1.3 74.7 - - - +
142B ARG* 1.3 61.7 + - + +
143B ASP 3.5 0.4 - - - -
146B ILE* 5.7 0.4 - - - -
147B TYR* 2.5 38.1 + - - +
153B VAL* 4.9 0.2 - - + -
155B LEU* 4.8 6.5 - - + -
171B ILE* 4.6 5.8 - - + -
172B LYS* 4.5 13.2 - - + -
185B ILE* 3.8 9.6 - - + +
189B LEU* 3.8 25.4 - - + -
191B TYR* 3.4 26.0 - - + +
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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