Contacts of the strand formed by residues 215 - 220 (chain A) in PDB entry 1FIU
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 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A HIS* 2.9 53.9 + + - -
182A ALA* 3.6 14.8 - - + -
183A SER 2.8 25.8 + - - -
214A PRO* 1.3 75.1 - - - +
216A ILE* 1.3 60.9 + - - +
217A VAL* 4.1 10.8 - - + -
239A ASP* 3.4 10.3 - - - +
283A ASP* 3.1 25.1 + - + -
284A LEU* 3.6 21.5 - - + -
286A VAL* 3.5 17.5 - - + +
212D ARG* 3.4 35.9 - - + +
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Residues in contact with ILE 216 (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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183A SER* 3.6 7.9 - - - +
198A ALA 5.2 0.4 - - - +
202A GLY* 3.8 30.5 - - - +
205A LEU* 3.9 29.8 - - + -
206A VAL* 4.4 0.2 - - + -
213A LEU* 3.8 26.2 - - + -
214A PRO* 3.5 8.3 - - + +
215A HIS* 1.3 78.4 - - - +
217A VAL* 1.3 61.6 + - - +
237A GLU 3.5 24.5 - - - +
238A ILE* 3.8 14.3 - - + -
239A ASP* 2.8 46.9 + - - +
209D ARG* 4.1 1.8 - - - +
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Residues in contact with VAL 217 (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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183A SER* 3.0 5.4 + - - +
184A ILE* 3.7 35.2 - - + -
185A SER* 2.9 25.5 + - - -
215A HIS* 4.7 11.7 - - + -
216A ILE* 1.3 88.7 - - - +
218A VAL* 1.3 68.0 + - - +
238A ILE* 4.6 0.9 - - - -
239A ASP* 4.3 9.4 - - + +
240A CYS 3.5 10.8 - - - +
242A TYR* 3.7 26.9 - - + +
280A LEU* 4.1 20.0 - - + -
284A LEU* 5.4 2.0 - - + -
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Residues in contact with VAL 218 (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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185A SER* 3.1 19.3 - - - +
187A LYS* 4.5 17.9 - - + -
190A ILE* 6.0 0.2 - - + -
198A ALA* 4.0 25.8 - - + -
217A VAL* 1.3 81.8 - - - +
219A VAL* 1.3 69.1 - - - +
220A THR* 4.8 4.3 - - - -
231A ILE* 4.3 11.7 - - + -
238A ILE* 4.0 21.3 - - + -
240A CYS 3.3 4.6 + - - -
241A VAL* 3.3 18.9 - - + +
242A TYR* 2.8 34.0 + - - +
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Residues in contact with VAL 219 (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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69A PHE* 3.7 8.4 - - + -
73A CYS* 3.7 31.0 - - + -
184A ILE* 4.0 15.5 - - + -
185A SER 2.7 9.4 + - - +
186A CYS* 3.3 6.1 - - - -
187A LYS 2.9 24.1 + - - -
217A VAL* 5.1 0.7 - - + -
218A VAL* 1.3 78.4 - - - +
220A THR* 1.3 65.7 + - - +
242A TYR* 3.2 17.9 - - + +
244A PHE* 5.0 4.7 - - + +
277A ILE* 3.9 17.0 - - + -
280A LEU* 3.8 28.5 - - + -
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Residues in contact with THR 220 (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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69A PHE* 3.9 6.1 - - - -
187A LYS* 2.8 22.2 + - - -
190A ILE* 3.6 22.9 - - + +
218A VAL* 4.8 4.3 - - - -
219A VAL* 1.3 77.1 - - - +
221A ALA* 1.3 60.1 + - - +
222A GLU* 3.1 22.7 + - + +
228A ILE* 4.5 6.5 - - + -
241A VAL* 4.2 17.7 - - + -
242A TYR 3.0 15.2 + - - +
243A HIS* 3.6 15.1 - - + -
244A PHE 2.9 24.9 + - - -
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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