Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 1FX7
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 ARG 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL 3.4 9.6 - - - +
166A VAL* 4.4 13.9 - - + +
192A ASN 3.8 3.1 + - - +
193A ALA* 1.3 74.6 - - - +
195A VAL* 1.3 67.2 + - - +
209A ILE* 5.2 4.3 - - - +
210A PRO* 5.4 4.5 - - - +
230A VAL* 4.5 21.1 - - + +
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Residues in contact with VAL 195 (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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164A ALA* 3.5 3.5 - - - +
165A VAL* 2.8 48.9 + - + +
167A VAL* 3.9 24.5 - - + -
188A GLY 5.3 0.7 - - - +
189A VAL* 4.4 11.9 - - + -
193A ALA* 4.9 3.8 - - + +
194A ARG* 1.3 79.1 - - - +
196A THR* 1.3 65.7 + - - +
197A VAL* 4.4 4.9 - - + -
207A ILE* 3.8 30.3 - - + -
208A VAL 3.9 4.5 - - - +
209A ILE* 3.9 22.7 - - + +
227A VAL* 5.9 0.2 - - + -
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 4.5 16.0 - - + +
163A VAL 3.2 9.9 - - - -
164A ALA* 4.3 14.4 - - + +
195A VAL* 1.3 80.2 - - - +
197A VAL* 1.3 64.1 - - - +
207A ILE* 3.6 1.2 - - - +
208A VAL* 2.9 57.6 + - + +
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Residues in contact with VAL 197 (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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154A LEU* 3.9 17.5 - - + -
157A LEU* 3.3 33.9 - - + -
162A PRO* 3.5 1.6 - - - +
163A VAL* 2.8 44.6 + - + +
165A VAL* 4.0 18.6 - - + -
195A VAL* 4.4 5.6 - - + -
196A THR* 1.3 80.1 - - - +
198A GLU* 1.3 62.8 + - - +
205A VAL* 3.7 11.7 - - + -
206A THR 3.3 2.7 - - - -
207A ILE* 4.0 23.3 - - + -
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Residues in contact with GLU 198 (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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160A GLY 4.8 6.5 - - - +
161A SER 5.1 2.7 - - - -
162A PRO* 4.3 30.5 - - + +
197A VAL* 1.3 76.9 - - - +
199A THR* 1.3 66.3 + - - +
200A THR* 5.6 0.2 - - - +
205A VAL* 3.4 4.1 - - - -
206A THR* 2.7 61.7 + - - +
208A VAL* 3.4 24.6 - - - +
214A ASN* 5.2 0.5 - - - +
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Residues in contact with THR 199 (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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154A LEU 5.4 0.2 + - - -
157A LEU* 3.7 23.6 + - - +
158A PRO 3.8 8.9 + - - -
159A ALA* 3.9 28.9 - - + +
160A GLY 4.8 8.2 + - - +
198A GLU* 1.3 77.1 - - - +
200A THR* 1.3 75.5 + - - +
201A PRO* 4.3 1.7 - - - +
203A GLY* 5.2 5.8 - - - -
204A GLY 3.7 8.1 - - - +
205A VAL* 4.4 9.6 - - + +
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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