Contacts of the strand formed by residues 250 - 258 (chain A) in PDB entry 5FS9
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 GLN 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 5.8 0.3 - - - +
129A PRO 4.3 0.5 - - - +
130A SER* 3.8 15.9 - - - +
242A MET* 3.7 34.4 - - + +
243A VAL 3.4 4.3 - - - +
244A LYS* 4.2 20.2 - - + +
248A GLY 3.6 8.7 + - - +
249A SER* 1.3 79.2 - - - +
251A ILE* 1.3 65.8 + - - +
252A THR* 4.3 0.4 - - - -
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 3.9 24.0 - - + -
129A PRO 3.7 18.6 - - - +
130A SER 3.5 5.8 - - - +
131A HIS* 4.4 0.4 - - - -
132A VAL* 4.0 21.1 - - + +
135A LEU* 4.7 5.4 - - + -
160A LEU* 3.9 20.6 - - + -
162A VAL* 4.4 7.0 - - + -
242A MET* 3.3 5.0 - - - -
243A VAL* 2.9 44.1 + - + +
245A LEU* 4.1 27.1 - - + -
249A SER 5.0 0.2 - - - -
250A GLN* 1.3 79.7 - - - +
252A THR* 1.3 72.2 + - - +
253A TYR* 4.5 1.6 - - - -
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Residues in contact with THR 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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130A SER 3.0 14.9 + - - +
131A HIS* 2.8 29.1 - - - +
132A VAL 2.9 25.3 + - - -
240A ASP 4.3 5.8 - - - +
241A ASN* 3.2 10.8 - - - +
242A MET* 3.7 33.2 - - + -
250A GLN 4.3 0.6 - - - -
251A ILE* 1.3 77.7 - - - +
253A TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 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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131A HIS* 4.0 4.2 + - - -
132A VAL 3.1 12.1 - - - +
135A LEU* 3.8 35.7 - - + -
236A LEU* 3.6 26.1 - - + +
238A VAL* 4.2 5.9 - - - -
241A ASN* 2.9 54.3 + - + +
242A MET* 3.5 10.0 + - - -
243A VAL* 4.1 3.1 - - + -
251A ILE 4.5 0.7 - - - -
252A THR* 1.3 75.8 - - - +
254A GLU* 1.3 65.7 + - - +
255A LYS 3.7 12.8 - - - +
256A CYS* 3.6 28.0 - - + -
432A ASN* 3.5 24.9 + - - -
433A ILE* 3.7 15.1 - - - +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A HIS* 2.8 33.9 - - + +
132A VAL 3.4 0.6 + - - -
133A PRO* 3.1 32.1 + - + +
253A TYR* 1.3 78.2 - - - +
255A LYS* 1.3 74.1 + - + +
432A ASN* 3.2 25.1 + - - +
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO 2.9 7.0 + - - +
134A PHE* 3.5 19.4 - - + -
135A LEU 2.9 24.4 + - - -
253A TYR* 3.7 4.9 - - - +
254A GLU* 1.3 87.6 - - + +
256A CYS* 1.3 61.9 + - - +
431A SER 5.6 0.9 - - - -
432A ASN* 3.6 11.0 - - + +
434A TRP* 3.8 27.0 - - + -
468A ASN 5.3 0.4 + - - -
469A MET* 3.0 45.4 + - + +
470A THR* 5.1 1.8 - - - +
471A GLY* 5.2 2.8 - - - +
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Residues in contact with CYS 256 (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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135A LEU* 3.2 17.3 - - - +
137A ILE* 3.5 32.1 - - - -
236A LEU* 4.8 5.4 - - - -
253A TYR* 3.6 32.8 - - + +
255A LYS* 1.3 75.8 - - - +
257A LEU* 1.3 65.3 + - - +
258A ILE* 4.2 7.0 - - - -
432A ASN 2.9 9.4 + - - +
433A ILE* 3.3 8.8 - - + -
434A TRP* 2.9 29.3 + - - -
469A MET* 3.7 4.0 - - - -
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Residues in contact with LEU 257 (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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135A LEU 2.8 7.1 + - - +
136A LEU* 3.9 14.8 - - + -
137A ILE* 2.8 33.8 + - - +
142A ALA 4.3 4.7 - - - +
143A ALA* 4.4 0.9 - - - -
146A ALA* 3.4 33.7 - - + -
256A CYS* 1.3 74.0 - - - +
258A ILE* 1.3 63.6 + - - +
259A ALA* 3.8 15.4 + - + -
434A TRP* 3.4 23.8 - - + +
436A ALA* 3.7 18.6 - - + +
465A ALA* 3.7 24.7 - - + -
469A MET* 3.7 14.5 - - + +
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Residues in contact with ILE 258 (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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137A ILE* 4.1 17.7 - - + -
236A LEU* 4.1 11.2 - - + -
256A CYS* 4.6 1.8 - - - -
257A LEU* 1.3 73.7 - - - +
259A ALA* 1.3 61.4 + - - +
260A THR* 3.8 20.0 - - + +
406A LEU* 5.0 6.7 - - + -
412A LEU* 3.6 31.2 - - + -
421A PHE* 3.6 37.7 - - + -
433A ILE* 4.0 14.8 - - + -
434A TRP 2.8 16.0 + - - +
435A VAL* 3.2 15.2 - - + +
436A ALA 3.1 24.1 + - - -
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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