Contacts of the strand formed by residues 316 - 323 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A TYR* 3.5 21.1 - - - -
258A ILE 3.3 9.2 - - - -
259A GLU* 3.8 2.3 - - - +
309A LYS* 3.6 5.5 - - - +
310A ASP* 2.9 24.6 + - - +
313A ALA 3.0 12.2 + - - +
314A GLU 3.3 2.3 - - - +
315A LYS* 1.3 75.2 - - - +
317A ILE* 1.3 69.3 + - - +
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Residues in contact with ILE 317 (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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140A VAL* 5.3 0.2 - - + -
256A VAL 3.8 0.5 - - - +
257A TYR* 3.4 6.3 - - - -
258A ILE* 2.9 43.5 + - + +
260A THR* 4.3 15.0 - - + +
264A ALA* 3.9 37.0 - - + +
266A ILE* 4.1 19.1 - - + -
269A VAL* 4.0 13.5 - - + -
307A ILE* 4.3 5.8 - - + -
308A ARG 3.4 10.3 - - - +
309A LYS* 4.8 1.6 - - + -
310A ASP 4.3 0.4 - - - +
315A LYS 4.4 4.5 - - - +
316A GLY* 1.3 80.2 - - - +
318A HIS* 1.3 74.7 + - - +
319A MET* 4.2 19.2 - - + +
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Residues in contact with HIS 318 (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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255A SER* 5.5 1.8 + - - -
256A VAL 3.3 6.4 + - - +
257A TYR* 3.3 25.3 - + - +
306A ARG 3.3 2.6 - - - +
307A ILE* 3.3 0.5 - - - -
308A ARG* 2.8 56.4 + - - +
310A ASP* 2.9 35.8 + - - -
317A ILE* 1.3 80.5 - - - +
319A MET* 1.3 66.0 + - - +
150B ILE* 4.0 19.4 - - + +
217B TYR* 3.4 19.7 - - - -
240B SER* 3.6 19.9 - - - -
241B ALA 5.2 0.9 - - - -
242B THR* 4.2 13.0 + - - +
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Residues in contact with MET 319 (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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136A ALA* 4.4 4.5 - - - -
137A LEU* 3.8 30.7 - - + -
140A VAL* 4.7 5.8 - - + -
255A SER* 3.7 5.7 + - - -
256A VAL* 3.0 47.1 + - + +
258A ILE* 4.2 10.8 - - + -
269A VAL* 4.7 3.1 - - + -
273A ILE* 4.4 15.9 - - + -
304A VAL* 3.9 18.8 - - + -
305A GLY 3.5 12.3 - - - +
306A ARG* 3.7 6.3 - - - -
307A ILE* 3.8 10.8 - - + -
308A ARG* 5.0 1.6 - - - -
317A ILE* 4.2 21.8 - - + +
318A HIS* 1.3 78.1 - - - +
320A TRP* 1.3 62.0 + - - +
321A VAL* 4.1 11.4 - - + -
242B THR* 5.5 2.8 + - - +
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Residues in contact with TRP 320 (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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154A TYR* 3.7 26.9 - + - -
253A SER* 3.3 30.1 - - - -
254A GLU 3.4 19.7 - - - -
255A SER* 3.9 13.0 - - - -
291A PRO* 3.0 43.0 + - + +
292A GLN* 5.1 0.2 - - - +
303A PHE 3.7 0.5 - - - +
304A VAL* 3.3 5.9 - - - +
305A GLY 2.8 37.3 + - - +
306A ARG* 3.8 14.4 - - + -
319A MET* 1.3 72.9 - - - +
321A VAL* 1.3 61.2 + - - +
322A VAL* 3.6 7.8 - - + +
205B ALA* 3.9 18.3 + - + -
207B PRO* 3.4 26.6 - - + +
242B THR* 4.6 6.3 - - + -
244B VAL* 3.7 38.1 - - + -
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Residues in contact with VAL 321 (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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132A GLN* 3.1 41.3 + - + +
133A MET* 5.4 0.7 - - - -
136A ALA* 3.8 22.0 - - + -
137A LEU* 6.3 0.2 - - + -
253A SER* 3.3 1.7 - - - -
254A GLU* 2.9 41.4 + - - +
256A VAL* 3.9 20.9 - - + -
302A THR* 3.7 16.2 - - + -
303A PHE 3.3 3.8 - - - +
304A VAL* 4.2 2.7 - - + -
319A MET* 4.1 13.2 - - + -
320A TRP* 1.3 79.6 - - - +
322A VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 322 (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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132A GLN* 4.0 2.2 - - - -
251A ALA* 4.3 2.2 - - + -
252A HIS 3.3 9.6 - - - +
253A SER* 3.6 17.5 - - - +
291A PRO* 3.6 22.7 - - + -
292A GLN 3.9 2.0 - - - +
293A ALA* 3.7 21.8 - - - +
296A ALA* 3.6 24.0 - - + -
302A THR* 3.6 1.6 - - - +
303A PHE* 2.8 42.4 + - + -
320A TRP* 3.6 23.3 - - - +
321A VAL* 1.3 80.5 - - - +
323A SER* 1.3 65.5 + - - +
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Residues in contact with SER 323 (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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132A GLN* 3.5 25.2 + - - +
251A ALA* 4.0 5.2 - - - -
252A HIS 3.0 27.9 + - - +
296A ALA* 4.5 2.7 - - - -
299A SER 4.9 0.5 + - - -
301A ASP 3.1 20.1 + - - -
302A THR* 3.4 18.4 + - - -
322A VAL* 1.3 79.8 - - - +
324A ASP* 1.3 65.6 + - - +
325A ASN 3.1 0.7 + - - -
328A LYS* 3.6 16.7 + - - +
329A GLY* 5.5 1.8 - - - -
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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