Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 4FGU
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 HIS 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 2.8 24.1 + - - +
29A HIS* 3.4 19.9 + + - +
30A TRP* 3.0 25.6 + - - +
138A GLN 3.6 17.4 + - - -
139A ASP* 1.3 71.8 - - - +
141A VAL* 1.3 61.4 + - - +
180A ARG* 3.6 20.2 + - - -
181A LYS* 3.7 26.2 - - + +
278A MET* 3.2 33.1 - - + +
282A GLN* 3.3 34.6 - - + +
283A PHE* 3.8 11.3 - + + -
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Residues in contact with VAL 141 (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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30A TRP* 3.4 15.0 - - + +
32A VAL* 5.5 0.7 - - + -
133A LEU* 4.2 23.1 - - + -
135A SER* 3.5 30.3 - - - +
139A ASP 4.0 1.3 + - - +
140A HIS* 1.3 78.5 - - - +
142A PHE* 1.3 68.2 + - - +
143A ILE* 4.4 11.4 - - + -
173A MET* 4.9 1.3 - - + -
178A MET 4.1 0.4 - - - +
179A TYR* 3.9 20.0 - - + -
181A LYS 3.4 6.2 + - - +
182A MET* 3.4 30.4 - - + -
183A VAL 3.3 20.8 + - - -
283A PHE* 3.9 4.1 - - - -
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Residues in contact with PHE 142 (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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30A TRP 3.0 8.4 + - - +
31A VAL* 3.2 22.7 - - + +
32A VAL 3.1 20.8 + - - -
52A ALA* 6.5 0.2 - - + -
56A ILE* 4.2 14.4 - - + -
141A VAL* 1.3 77.3 - - - +
143A ILE* 1.3 73.8 + - - +
144A TYR* 4.6 10.1 - - + -
182A MET* 5.1 0.4 - - - -
183A VAL* 3.4 33.7 - - + -
185A TYR* 3.1 40.2 - + + -
237A TRP* 4.3 16.4 - + - -
283A PHE* 3.5 31.9 - - + +
284A GLN* 4.2 17.9 - - + -
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Residues in contact with ILE 143 (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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32A VAL* 3.3 29.8 - - + +
113A PHE* 4.3 24.2 - - + -
117A LEU* 4.5 15.0 - - + -
141A VAL* 4.4 13.0 - - + -
142A PHE* 1.3 84.6 - - - +
144A TYR* 1.3 66.6 + - - +
145A PHE* 5.9 3.8 - - + -
166A LEU* 5.9 1.1 - - + -
182A MET* 5.4 1.3 - - - -
183A VAL 3.3 5.5 + - - -
184A PHE* 3.5 49.5 - - + -
185A TYR 3.2 25.5 + - - +
186A ILE* 5.7 4.9 - - + -
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Residues in contact with TYR 144 (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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32A VAL 2.9 12.0 + - - +
33A ILE* 3.8 25.8 - - + -
34A VAL* 2.9 28.2 + - - +
48A ASP* 3.9 17.1 - - - +
49A ALA 4.6 0.2 - - - -
52A ALA* 4.5 9.4 - - + -
113A PHE* 6.1 0.3 - - - -
142A PHE* 4.6 11.2 - - + -
143A ILE* 1.3 78.8 - - - +
145A PHE* 1.3 68.3 + - - +
146A THR* 3.2 31.8 - - + +
185A TYR* 3.3 25.4 - - + -
187A GLU* 4.5 5.2 - - + -
233A TYR* 5.2 1.1 - + - -
234A SER* 2.4 34.5 + - - -
237A TRP* 3.4 35.2 - + - -
238A MET* 4.0 3.3 - - + +
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Residues in contact with PHE 145 (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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34A VAL* 3.3 19.5 - - + -
36A GLY 4.6 4.3 - - - -
113A PHE* 6.2 3.1 - + - -
143A ILE* 5.9 4.3 - - + -
144A TYR* 1.3 80.1 - - - +
146A THR* 1.3 60.8 + - - +
147A ASP* 3.8 24.5 - - + -
148A HIS 4.4 2.2 - - - -
154A LEU* 3.6 47.8 - - + -
155A VAL 3.4 21.8 - - - -
156A PHE* 3.7 28.9 - + - -
161A LEU* 6.4 0.2 - - + -
185A TYR 3.4 4.9 + - - -
186A ILE* 4.1 20.6 - - + -
187A GLU* 2.8 37.8 + - - +
188A ALA* 4.3 5.8 - - + -
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Residues in contact with THR 146 (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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34A VAL 3.0 13.3 + - - -
35A ALA* 3.3 5.9 - - - +
36A GLY 3.2 15.3 + - - -
45A HIS* 3.1 36.5 + - + +
48A ASP* 3.6 15.6 - - + +
49A ALA* 4.3 2.8 + - - +
144A TYR* 3.2 37.5 - - + +
145A PHE* 1.3 71.7 - - - +
147A ASP* 1.3 65.5 + - - +
187A GLU* 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