Contacts of the strand formed by residues 314 - 322 (chain B) 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 THR 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B LEU 3.1 7.4 + - - +
176B ARG* 3.4 15.5 - - + +
177B TYR* 2.8 27.9 + - - +
313B ALA* 1.3 77.6 - - - +
315B PHE* 1.3 63.3 + - - +
350B GLU* 3.0 27.2 + - + +
351B SER* 3.3 25.8 - - - +
352B VAL 4.0 0.2 - - - -
353B LYS* 3.9 19.5 - - + +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 3.5 41.5 - + + -
179B LEU* 5.9 2.0 - - + -
303B PHE* 4.0 17.5 - + - -
313B ALA* 3.6 20.0 - - + -
314B THR* 1.3 76.7 - - - +
316B ILE* 1.3 62.1 + - - +
317B ILE* 4.1 19.2 + - + +
331B MET* 5.3 0.3 - - - +
349B SER 3.9 2.4 - - - +
350B GLU* 3.5 4.0 - - - -
351B SER* 2.7 43.7 + - - +
354B MET* 3.8 24.2 - - + -
355B SER 4.4 1.3 - - - -
356B THR* 3.8 20.0 - - + -
359B VAL* 3.4 38.8 - - + -
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Residues in contact with ILE 316 (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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176B ARG* 4.0 23.3 - - - +
177B TYR 3.0 15.5 + - - +
178B GLU* 4.2 25.5 - - + +
179B LEU 2.8 30.0 + - - +
315B PHE* 1.3 77.9 - - - +
317B ILE* 1.3 64.3 + - - +
318B LYS* 5.0 2.7 - - + -
347B GLU* 4.4 20.4 - - + +
348B PHE 4.2 10.5 - - - +
349B SER 4.7 2.5 - - - -
350B GLU* 3.8 30.7 - - + +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.4 24.7 - - + +
181B LEU* 5.0 0.4 - - + -
315B PHE* 4.3 17.9 + - + +
316B ILE* 1.3 80.5 - - - +
318B LYS* 1.3 64.5 + - - +
319B ILE* 4.1 26.7 - - + -
329B SER* 3.7 24.9 - - - +
330B ASN* 5.7 1.8 - - + +
347B GLU* 3.5 2.3 - - - +
348B PHE* 3.1 44.0 + - + +
349B SER 5.1 0.8 + - - +
359B VAL* 4.0 25.6 - - + -
361B PHE* 4.3 9.9 - - + -
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Residues in contact with LYS 318 (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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178B GLU* 3.5 25.5 + - + +
179B LEU 2.8 9.8 + - - +
180B SER* 3.4 27.1 - - - -
181B LEU* 2.5 32.8 + - - -
316B ILE* 5.0 4.5 - - + +
317B ILE* 1.3 74.4 - - - +
319B ILE* 1.3 64.7 + - - +
345B GLN* 3.8 24.2 - - - +
346B ASP 3.2 5.8 - - - +
347B GLU* 3.9 30.5 - - + -
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 3.5 31.2 - - + -
183B PRO* 4.1 9.4 - - + -
317B ILE* 4.1 17.7 - - + -
318B LYS* 1.3 83.3 - - - +
320B ILE* 1.3 74.9 + - - +
321B ARG* 4.1 2.8 + - + +
327B ALA* 4.3 12.1 - - + -
328B LEU 5.7 0.2 - - - +
344B VAL 3.6 0.7 - - - +
345B GLN* 3.5 1.9 - - - -
346B ASP* 2.6 51.5 + - + +
348B PHE* 4.1 12.1 - - + -
361B PHE* 4.4 19.1 - - + -
363B VAL* 4.0 24.9 - - + -
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Residues in contact with ILE 320 (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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180B SER* 6.5 1.3 - - - -
181B LEU 2.9 14.1 + - - +
182B HIS* 3.2 44.7 - - + +
183B PRO* 3.1 28.2 - - - +
319B ILE* 1.3 72.0 - - - +
321B ARG* 1.3 63.2 + - - +
339B LEU* 4.8 12.1 - - + -
343B LEU* 3.8 20.2 - - + -
344B VAL 3.2 11.9 - - - +
345B GLN* 3.7 32.3 - - + +
1M NAG 4.3 0.8 - - + +
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Residues in contact with ARG 321 (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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183B PRO 5.3 0.7 - - - -
319B ILE* 4.6 7.9 - - + +
320B ILE* 1.3 74.5 - - - +
322B ASP* 1.3 63.2 + - - +
323B GLU* 3.4 30.1 + - - +
325B TYR* 2.9 32.6 + - + -
326B THR* 4.3 1.1 - - - -
327B ALA* 3.8 21.5 - - + +
333B LYS* 5.5 2.0 - - - +
336B SER* 4.0 5.3 + - - -
343B LEU* 3.6 3.9 - - - -
344B VAL* 2.9 53.8 + - + +
346B ASP* 3.0 34.6 + - - +
363B VAL* 4.4 17.9 - - + -
1M NAG 3.9 10.3 - - - -
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Residues in contact with ASP 322 (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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185B LEU* 5.7 2.8 + - - +
186B THR* 5.7 0.7 + - - -
321B ARG* 1.3 84.2 + - - +
323B GLU* 1.3 66.2 + - - +
324B GLN* 3.2 25.4 - - + +
325B TYR* 3.2 35.9 + - + +
342B GLY 5.1 0.7 - - - -
343B LEU* 3.2 12.6 - - - +
1M NAG 2.9 54.2 + - - +
2M NAG 5.2 1.1 + - - +
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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