Contacts of the strand formed by residues 248 - 253 (chain A) in PDB entry 4F5G
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.4 14.1 - - + -
99A LEU* 5.1 0.7 - - + -
217A LEU* 4.2 2.5 - - - -
218A PRO* 3.6 34.8 - - + +
220A ILE* 5.1 5.4 - - + -
238A LEU* 4.4 6.1 - - + +
241A PHE* 3.9 12.1 - - + -
242A ALA* 3.5 35.2 - - + +
245A HIS* 3.9 14.4 - - + +
247A GLU* 1.3 82.9 - - - +
249A ILE* 1.3 72.8 + - - +
250A VAL* 4.8 7.6 - - + -
269A THR 3.9 0.4 - - - +
270A LEU* 3.8 0.7 - - - -
271A VAL* 2.9 44.8 + - + +
12B PHE* 4.2 1.4 - - - -
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Residues in contact with ILE 249 (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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120A ALA* 4.1 10.1 - - + -
123A PHE* 4.8 1.3 - - + -
124A LEU* 3.9 29.2 - - + -
184A VAL* 5.4 0.4 - - + -
217A LEU* 3.9 24.0 - - + -
218A PRO 3.1 7.2 + - - +
219A LEU* 3.3 26.1 - - + -
220A ILE* 2.9 25.5 + - - +
248A LEU* 1.3 78.2 - - - +
250A VAL* 1.3 70.2 + - - +
251A ALA* 4.7 0.9 - - + +
268A CYS* 3.8 27.6 - - - -
269A THR 3.3 4.7 - - - +
270A LEU* 3.8 15.9 - - + -
12B PHE* 3.9 10.5 - - + -
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Residues in contact with VAL 250 (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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92A LEU* 3.7 26.7 - - + -
93A PHE* 4.3 20.9 - - + -
220A ILE* 3.4 18.4 - - + +
222A ILE* 3.8 21.1 - - + -
238A LEU* 4.0 20.0 - - + -
248A LEU* 4.8 9.2 - - + -
249A ILE* 1.3 84.3 - - - +
251A ALA* 1.3 64.8 + - - +
252A SER* 3.9 1.0 + - - -
267A ALA 3.4 1.6 - - - +
268A CYS* 3.4 5.0 - - - -
269A THR* 2.8 38.8 + - + +
271A VAL* 5.6 0.2 - - + -
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Residues in contact with ALA 251 (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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113A GLY* 4.2 4.3 - - - +
116A ALA* 3.9 15.5 - - + +
117A LEU* 3.7 38.4 - - + +
120A ALA* 6.0 0.4 - - + -
219A LEU* 4.3 6.1 - - + +
220A ILE 2.9 9.7 + - - +
221A ASP* 3.5 6.1 - - - +
222A ILE* 2.9 26.2 + - - +
249A ILE* 4.2 2.6 - - + -
250A VAL* 1.3 71.7 - - - +
252A SER* 1.3 60.9 + - - +
267A ALA 3.4 4.9 - - - -
268A CYS* 5.8 0.2 - - - -
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Residues in contact with SER 252 (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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84A PHE* 5.9 0.3 - - - -
88A THR* 3.6 22.7 - - - +
92A LEU* 4.2 15.4 - - - +
113A GLY* 3.5 8.8 - - - -
222A ILE* 3.2 20.9 - - - -
250A VAL* 3.8 4.6 + - - -
251A ALA* 1.3 76.0 - - - +
253A SER* 1.3 63.6 + - - +
254A CYS* 6.0 1.7 - - - -
266A GLY* 3.0 4.2 - - - -
267A ALA* 2.9 37.8 + - - +
269A THR* 5.2 0.3 + - - -
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Residues in contact with SER 253 (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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113A GLY* 3.9 2.7 - - - -
222A ILE 3.1 9.9 + - - +
223A ALA* 3.8 32.2 - - - +
252A SER* 1.3 78.5 - - - +
254A CYS* 1.3 62.0 + - - +
255A SER* 2.8 21.6 + - - -
256A LLP 2.5 33.5 + - - -
257A ASN* 3.6 15.8 + - - +
265A VAL 3.8 4.0 + - - -
266A GLY* 4.0 0.4 - - - -
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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