Contacts of the strand formed by residues 242 - 251 (chain A) in PDB entry 5MJ6
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.5 30.2 - - + -
163A TRP* 3.6 21.3 - - - +
165A GLN 3.2 21.6 + - - +
166A ILE* 3.7 17.6 + - - +
168A LEU* 4.3 6.5 - - + +
208A ILE* 3.9 5.3 - - + +
209A LEU 3.2 9.2 - - - +
210A HIS* 3.8 15.7 + - + +
211A SER 4.8 0.5 - - - +
236A GLU* 4.6 0.2 - - - +
237A TYR* 2.9 34.6 + - - +
240A HIS* 3.1 30.2 + - + +
241A GLY* 1.3 78.8 - - - +
243A ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 243 (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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161A PHE* 3.7 4.0 - - - -
207A ILE 3.7 0.7 - - - +
208A ILE* 3.5 4.0 - - - +
209A LEU* 2.9 63.3 + - + +
211A SER* 3.7 39.5 - - - +
216A ILE* 4.5 4.5 - - + -
234A ILE* 4.0 25.1 - - + -
235A LEU 3.3 13.2 - - - +
236A GLU* 4.5 14.6 - - + +
241A GLY 4.3 0.2 + - - -
242A GLN* 1.3 80.1 - - - +
244A ALA* 1.3 62.2 + - - +
245A ILE* 4.3 6.1 - - + -
261A ILE* 4.3 10.5 - - + -
304A PRO* 4.4 2.0 - - + -
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Residues in contact with ALA 244 (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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161A PHE* 3.6 18.4 - - + -
162A PRO* 3.8 15.7 - - + -
206A ASN* 5.2 1.3 - - + -
207A ILE 3.3 4.0 - - - +
208A ILE* 3.7 20.9 - - + -
233A GLU 3.6 0.2 - - - +
234A ILE* 3.3 6.4 - - - +
235A LEU* 2.9 38.2 + - + +
243A ILE* 1.3 76.0 - - - +
245A ILE* 1.3 65.4 + - - +
246A VAL* 3.7 2.9 + - + -
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Residues in contact with ILE 245 (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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206A ASN* 3.5 3.1 - - - -
207A ILE* 2.8 55.4 + - + +
209A LEU* 4.0 16.8 - - + -
219A VAL* 4.1 19.3 - - + -
221A PHE* 5.1 4.0 - - + -
232A ALA* 3.7 26.7 - - + -
233A GLU 3.3 5.4 - - - +
234A ILE* 4.7 6.5 - - + -
243A ILE* 4.3 14.1 - - + -
244A ALA* 1.3 73.7 - - - +
246A VAL* 1.3 65.5 + - - +
247A ALA* 3.7 3.5 + - - +
259A LEU* 3.8 35.0 - - + -
261A ILE* 4.4 4.7 - - + -
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Residues in contact with VAL 246 (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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162A PRO* 5.4 0.4 - - + -
205A TRP* 3.6 9.4 - - + +
206A ASN* 3.9 22.0 - - - +
232A ALA* 3.8 5.9 - - - +
233A GLU* 3.0 41.8 + - + +
235A LEU* 4.1 29.4 - - + -
244A ALA* 4.5 4.5 - - + +
245A ILE* 1.3 73.2 - - - +
247A ALA* 1.3 70.1 + - - +
248A PRO* 4.0 0.5 - - - +
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Residues in contact with ALA 247 (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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205A TRP* 2.9 30.8 + - - +
207A ILE* 5.6 1.8 - - + -
221A PHE* 3.9 9.9 - - + -
245A ILE* 3.7 6.2 + - + +
246A VAL* 1.3 78.9 - - - +
248A PRO* 1.3 73.9 - - + +
249A GLU 3.2 18.6 + - - +
251A LEU* 3.6 23.6 - - + -
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Residues in contact with PRO 248 (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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205A TRP* 3.9 7.6 - - - -
221A PHE* 3.7 23.6 - - + -
230A LYS* 4.5 21.3 - - + -
231A GLN 4.7 6.3 - - - +
232A ALA* 4.5 10.5 - - + -
246A VAL 4.0 4.2 - - - +
247A ALA* 1.3 89.0 - - + +
249A GLU* 1.3 68.0 + - + +
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Residues in contact with GLU 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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205A TRP* 3.5 12.2 - - - -
221A PHE* 4.9 2.5 - - - -
223A SER* 6.0 1.6 - - - +
247A ALA* 3.2 20.6 - - - +
248A PRO* 1.3 88.5 - - + +
250A ALA* 1.3 71.9 + - - +
251A LEU* 4.0 2.3 - - - +
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Residues in contact with ALA 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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203A VAL* 4.7 10.1 - - + -
204A THR 3.7 7.0 - - - +
205A TRP* 3.1 45.2 - - + +
249A GLU* 1.3 80.3 + - - +
251A LEU* 1.3 67.5 + - - +
252A LEU* 3.6 18.7 + - + +
257A TYR* 4.0 4.2 + - - -
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Residues in contact with LEU 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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172A VAL* 3.8 23.3 - - + -
198A VAL* 5.6 0.7 - - + -
200A ALA* 3.9 13.0 - - + -
202A GLN 3.7 0.5 - - - +
203A VAL* 3.3 9.0 - - - +
204A THR* 2.8 45.1 + - + +
205A TRP 5.4 0.9 - - - -
206A ASN 5.0 0.7 - - - +
207A ILE* 3.7 29.2 - - + -
221A PHE* 3.5 27.4 - - + -
247A ALA* 3.6 20.2 - - + -
249A GLU 4.0 2.0 - - - +
250A ALA* 1.3 71.7 - - - +
252A LEU* 1.3 60.2 + - - +
257A TYR* 3.4 24.2 - - + -
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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