Contacts of the strand formed by residues 283 - 292 (chain B) in PDB entry 4MDH
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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 4.2 3.4 - - + -
271B ILE* 2.8 23.1 - - - +
272B SER* 3.0 26.7 + - - +
279B VAL* 4.5 0.4 - - + -
280B PRO* 3.6 30.5 - - + +
281B ASP 3.1 0.6 - - - +
282B ASP* 1.3 86.2 - - - +
284B LEU* 1.3 57.6 + - - +
285B TYR* 3.6 14.8 - - + -
316B ALA* 3.6 32.5 - - + +
319B LEU* 3.8 18.4 - - + +
320B ALA* 3.9 24.5 - - + +
323B LYS* 4.1 16.4 - - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN* 2.7 43.4 + - - +
136B CYS* 3.7 33.7 - - + +
137B LEU* 4.1 30.0 - - + +
140B SER* 5.4 2.5 - - - -
151B PHE* 4.5 9.6 - - + +
153B CYS* 3.5 32.5 - - - -
269B GLY 3.6 19.7 - - - +
270B ILE* 3.3 19.3 - - - +
271B ILE* 4.1 8.5 - - + +
283B LEU* 1.3 69.2 - - - +
285B TYR* 1.3 52.7 - - - +
319B LEU* 2.8 21.4 - - + +
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TRP* 4.0 12.6 - + - +
184B GLY* 3.5 27.2 + - - -
269B GLY* 3.8 3.4 - - - -
270B ILE 2.7 27.5 + - - +
272B SER* 4.4 2.0 - - - -
279B VAL* 3.5 37.3 - - + +
283B LEU* 3.6 14.6 - - + -
284B LEU* 1.3 75.5 - - - +
286B SER* 1.3 72.7 + - - +
287B PHE* 3.3 36.5 - + + -
312B MET* 3.0 32.8 + - - +
315B THR* 3.2 17.1 - - + +
316B ALA* 3.9 12.8 - - + -
319B LEU* 3.5 17.0 - - + -
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 4.9 0.2 - - - -
155B THR* 3.0 31.0 + - - +
182B ILE 2.7 25.1 + - - -
183B TRP* 3.5 9.6 - - - -
184B GLY 2.9 37.1 + - - -
268B MET 3.9 3.5 + - - -
269B GLY* 3.5 15.7 - - - -
285B TYR* 1.3 84.2 - - - +
287B PHE* 1.3 60.2 + - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ILE* 4.7 0.9 - - - -
182B ILE 4.3 4.7 - - - -
183B TRP* 3.9 17.0 - + - -
266B VAL 3.4 0.5 - - - +
267B SER* 3.3 7.8 - - - -
268B MET 3.1 30.4 + - - +
270B ILE* 4.2 15.0 - - + -
272B SER* 3.7 31.0 - - - -
275B ASN* 3.4 31.4 - - + -
277B TYR* 4.3 6.1 - + - -
279B VAL* 4.4 5.4 - - + -
285B TYR* 3.3 46.9 - + + -
286B SER* 1.3 75.8 + - - +
288B PRO* 1.3 77.0 - - + +
289B VAL* 3.6 4.4 + - + +
298B ILE* 4.1 28.3 - - + -
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Residues in contact with PRO 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ILE* 3.9 26.7 - - + -
183B TRP* 3.7 31.0 - - + -
265B PHE* 4.0 16.8 - - + -
266B VAL 3.7 6.5 - - - +
267B SER* 4.9 0.2 - - - -
277B TYR* 5.1 0.4 - - + -
287B PHE* 1.3 92.2 - - + +
289B VAL* 1.3 59.6 + - - +
298B ILE* 3.4 9.5 - - + +
299B VAL* 2.9 39.6 + - + +
302B LEU* 3.9 10.1 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR* 4.4 0.3 + - - -
265B PHE* 3.0 19.8 - - - +
266B VAL* 2.9 26.1 + - + +
268B MET* 4.3 15.5 - - + +
270B ILE* 4.0 28.9 - - + -
287B PHE 4.2 6.5 - - - +
288B PRO* 1.3 79.9 - - - +
290B THR* 1.3 65.5 + - - +
291B ILE* 3.9 16.4 - - + -
296B TRP* 3.5 25.4 - - + -
297B LYS 3.4 6.5 - - - +
298B ILE* 3.9 16.8 - - + +
299B VAL* 4.1 1.3 - - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B THR* 3.7 5.6 - - - +
264B GLU 3.7 22.9 - - - +
265B PHE* 3.8 9.0 - - + -
289B VAL* 1.3 74.3 - - - +
291B ILE* 1.3 63.9 + - - +
296B TRP* 3.0 5.9 - - - -
297B LYS* 2.8 47.4 + - - +
299B VAL* 4.2 10.6 + - + +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B ASP* 3.6 35.2 - - + +
256B ILE* 3.9 17.5 - - + +
259B GLY* 3.2 8.0 - - - -
260B THR* 3.1 42.5 + - - +
266B VAL* 4.0 16.2 - - + -
268B MET* 4.8 10.5 - - + -
289B VAL* 3.9 21.5 - - + -
290B THR* 1.3 79.1 - - - +
292B LYS* 1.3 62.8 + - - +
294B LYS* 4.0 2.9 - - - +
295B THR 3.0 22.0 - - - +
296B TRP* 4.0 9.0 - - + -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TRP 5.5 0.9 - - - +
258B PHE 4.3 5.4 - - - +
259B GLY* 4.1 12.0 + - - -
291B ILE* 1.3 74.5 - - - +
293B ASP* 1.3 74.4 + - - +
294B LYS 3.4 3.8 + - - -
295B THR* 2.9 14.0 + - - +
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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