Contacts of the strand formed by residues 316 - 323 (chain B) in PDB entry 4R54
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 GLY 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B TYR* 3.5 21.8 - - - -
258B ILE 3.2 9.9 - - - -
259B GLU* 3.7 3.0 - - - +
309B LYS* 3.7 4.9 - - - +
310B ASP* 3.0 25.2 + - - +
313B ALA 3.2 12.7 + - - +
314B GLU 4.7 1.9 - - - +
315B LYS* 1.3 78.5 - - - +
317B ILE* 1.3 64.3 + - - +
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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
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140B VAL* 5.1 0.4 - - + -
256B VAL 3.9 0.5 - - - +
257B TYR* 3.4 4.9 - - - -
258B ILE* 2.8 44.7 + - + +
260B THR* 4.3 16.8 - - + +
264B ALA* 4.2 16.4 - - + +
266B ILE* 4.0 21.8 - - + -
269B VAL* 3.9 28.3 - - + -
307B ILE* 4.3 6.5 - - + -
308B ARG 3.4 9.2 - - - +
309B LYS* 5.7 0.7 - - + -
310B ASP 4.2 0.4 - - - +
315B LYS 4.5 4.0 - - - +
316B GLY* 1.3 79.2 - - - +
318B HIS* 1.3 79.1 + - - +
319B MET* 4.2 17.0 - - + +
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Residues in contact with HIS 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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150A ILE* 3.9 20.2 - - + +
217A TYR* 3.5 20.4 - + - -
240A SER* 3.5 20.3 - - - -
241A ALA 5.2 1.8 - - - -
242A THR* 4.4 11.0 + - - +
255B SER* 5.6 2.2 + - - +
256B VAL 3.3 7.3 + - - +
257B TYR* 3.3 26.1 - + - +
306B ARG 3.2 3.1 - - - +
307B ILE* 3.4 0.9 - - - -
308B ARG* 2.9 56.4 + - - +
310B ASP* 2.9 35.6 + - - -
317B ILE* 1.3 81.2 - - - +
319B MET* 1.3 64.3 + - - +
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Residues in contact with MET 319 (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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242A THR* 5.5 2.1 + - - +
136B ALA* 4.4 4.3 - - - -
137B LEU* 3.9 29.4 - - + -
140B VAL* 4.9 4.0 - - + -
254B GLU 3.6 0.7 - - - +
255B SER* 3.6 5.0 + - - -
256B VAL* 2.9 47.4 + - + +
258B ILE* 4.2 10.5 - - + -
269B VAL* 4.9 2.9 - - + -
273B ILE* 4.3 17.0 - - + -
304B VAL* 3.8 21.1 - - + -
305B GLY 3.4 13.5 - - - +
306B ARG* 3.7 5.4 - - - -
307B ILE* 4.1 9.6 - - + -
308B ARG* 4.3 2.4 + - - +
317B ILE* 4.2 21.5 - - + -
318B HIS* 1.3 77.4 - - - +
320B TRP* 1.3 61.5 + - - +
321B VAL* 4.0 12.1 - - + -
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Residues in contact with TRP 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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205A ALA* 4.1 16.7 + - + -
207A PRO* 3.4 25.0 - - + +
242A THR* 4.6 5.8 - - + -
244A VAL* 3.7 34.3 - - + -
154B TYR* 3.7 30.1 - + - -
253B SER* 3.3 31.2 - - - -
254B GLU 3.3 20.6 - - - -
255B SER* 3.8 13.7 - - - -
291B PRO* 3.1 44.9 + - + +
304B VAL* 3.4 4.9 - - - +
305B GLY 2.8 36.5 + - - +
306B ARG* 3.8 15.0 - - + -
319B MET* 1.3 74.8 - - - +
321B VAL* 1.3 59.3 + - - +
322B VAL* 3.5 7.9 - - + +
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Residues in contact with VAL 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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132B GLN* 3.1 39.7 + - + +
133B MET* 4.7 1.1 - - - +
136B ALA* 3.7 22.0 - - + -
137B LEU* 6.3 0.2 - - + -
253B SER* 3.3 1.0 - - - -
254B GLU* 2.8 46.1 + - - +
256B VAL* 3.9 19.5 - - + -
302B THR* 3.7 17.5 - - + -
303B PHE 3.4 4.0 - - - +
304B VAL* 4.2 3.1 - - + -
319B MET* 4.0 13.2 - - - -
320B TRP* 1.3 79.0 - - - +
322B VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 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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132B GLN* 4.0 1.3 - - - -
251B ALA* 4.4 2.5 - - + -
252B HIS 3.3 9.6 - - - +
253B SER* 3.5 18.6 - - - +
291B PRO* 3.6 22.0 - - + -
292B GLN 3.9 1.6 - - - -
293B ALA* 3.8 22.9 - - - +
296B ALA* 3.6 24.0 - - + -
302B THR* 3.7 1.4 - - - -
303B PHE* 2.8 39.8 + - + +
320B TRP* 3.5 23.3 - - - +
321B VAL* 1.3 80.7 - - - +
323B SER* 1.3 65.1 + - - +
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 3.5 23.6 + - - +
251B ALA* 3.2 5.6 - - - -
252B HIS 2.9 30.3 + - - +
296B ALA* 4.4 4.3 - - - -
299B SER 4.7 0.9 + - - -
301B ASP 3.1 19.4 + - - -
302B THR* 3.6 13.8 + - - -
322B VAL* 1.3 78.5 - - - +
324B ASP* 1.3 69.9 + - - +
325B ASN 3.2 0.3 + - - -
328B LYS* 3.5 22.2 + - - +
329B GLY* 5.5 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