Contacts of the strand formed by residues 134 - 139 (chain B) in PDB entry 4FDI
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 VAL 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLY 4.5 1.3 - - - +
133B TYR* 1.3 76.1 - - - +
135B SER* 1.3 62.8 + - - +
157B ASP* 3.4 22.9 - - + +
158B GLU* 4.7 4.0 - - - +
216B PHE* 3.5 16.9 - - + -
220B GLN* 3.7 36.8 - - + +
224B HIS* 3.9 23.3 - - + +
225B PRO 3.0 7.2 + - - +
226B PHE* 3.4 4.2 - - - -
227B PHE 2.9 20.8 + - - -
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.7 19.9 + - - +
128B LEU* 4.8 0.3 - - - +
133B TYR* 4.4 7.8 - - - +
134B VAL* 1.3 74.1 - - - +
136B LYS* 1.3 61.7 + - - +
155B GLY 4.1 7.4 - - - -
156B PHE* 3.8 12.3 - - - -
157B ASP* 2.9 35.9 + - - +
158B GLU* 3.2 6.6 + - - +
216B PHE* 4.1 1.8 - - - -
227B PHE* 3.1 37.4 - - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 1.3 75.5 - - - +
137B ILE* 1.3 70.3 + - - +
138B VAL* 4.0 19.7 - - + -
156B PHE* 3.4 7.1 - - - -
158B GLU* 3.2 41.6 + - + +
159B TRP 4.5 1.3 - - - +
160B PHE 4.4 12.1 - - - +
182B ARG* 4.4 6.4 - - - +
183B ASP* 5.7 0.2 - - - -
212B GLU* 2.9 34.8 + - - -
215B ASP* 5.9 0.6 - - - +
216B PHE* 3.7 37.9 - - + -
219B ARG* 3.6 11.3 - - - +
227B PHE 2.9 6.9 + - - -
228B LEU* 3.6 4.7 - - + +
229B TYR 2.8 26.9 + - - -
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Residues in contact with ILE 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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136B LYS* 1.3 76.7 - - - +
138B VAL* 1.3 69.3 + - - +
139B GLY 4.3 0.2 - - - +
140B LYS 4.0 4.9 - - - +
141B TRP* 3.7 40.2 - - + +
151B PRO* 4.0 5.8 - - + -
156B PHE* 3.4 31.8 - - + -
158B GLU 3.1 10.3 + - - +
159B TRP* 3.3 37.6 - - + +
160B PHE 3.1 22.3 + - - -
229B TYR* 3.4 31.2 - - + +
231B ALA* 5.2 0.2 - - + -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 4.0 13.4 - - + -
137B ILE* 1.3 78.8 - - - +
139B GLY* 1.3 60.1 + - - +
160B PHE 3.3 6.1 - - - +
209B TYR* 3.7 35.7 - - + +
212B GLU* 3.8 24.0 - - + -
228B LEU* 3.9 20.0 - - + -
229B TYR 2.8 9.5 + - - +
230B TRP* 3.6 28.3 - - + +
231B ALA* 2.7 34.7 + - - +
232B VAL* 5.4 0.7 - - + -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.1 1.7 - - - +
138B VAL* 1.3 75.9 - - - +
140B LYS* 1.3 62.5 + - - -
159B TRP* 3.2 22.5 + - - -
160B PHE 2.7 15.9 + - - -
161B GLY* 4.0 3.1 - - - -
162B SER 3.3 10.2 + - - +
209B TYR* 4.0 24.7 - - - -
231B ALA 3.4 7.9 - - - -
233B ASP* 6.0 0.2 - - - -
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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