Contacts of the strand formed by residues 247 - 256 (chain A) in PDB entry 4E4Z
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A THR* 3.2 21.9 + - - -
244A HIS 3.3 7.5 + - - -
245A HIS 4.3 0.5 - - - +
246A LEU* 1.3 78.2 - - - +
248A LYS* 1.3 64.7 + - - +
268A PRO* 3.7 5.5 - - - +
269A GLN* 2.7 30.1 + - - +
294A VAL 3.7 1.6 - - - -
295A PHE* 3.7 17.4 - - - -
313A GLU* 3.9 0.4 + - - -
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A HIS 4.9 7.7 + - - -
246A LEU 4.0 5.2 - - - +
247A GLY* 1.3 78.6 + - - +
249A VAL* 1.3 62.0 + - + +
267A ASN* 3.5 15.2 - - - +
268A PRO* 3.4 12.3 - - - +
269A GLN* 6.0 3.2 - - + +
294A VAL* 2.8 29.6 + - + +
295A PHE 4.7 1.6 - - - -
296A THR* 3.6 35.3 - - + +
353A PRO* 4.8 23.7 - - + +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 5.6 0.2 - - - +
248A LYS* 1.3 81.0 - - + +
250A VAL* 1.3 69.9 + - - +
251A SER* 4.2 12.6 - - - +
265A ARG* 4.5 9.9 - - - +
266A GLN 3.6 19.7 - - - +
267A ASN* 5.1 0.2 - - - -
268A PRO* 3.8 0.7 - - - -
292A ARG 3.8 0.6 - - - +
293A CYS* 3.3 2.9 - - - -
294A VAL* 2.8 42.5 + - + +
349A GLU 4.9 0.2 - - - +
350A ALA 3.3 27.8 - - - +
351A ASN 4.7 1.8 - - - -
352A ILE 4.1 23.8 - - - +
353A PRO* 4.4 6.7 - - + -
354A ILE* 4.7 7.2 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 3.6 36.6 - - + +
242A HIS 5.1 0.7 - - - +
243A THR* 3.7 29.8 - - + -
249A VAL* 1.3 80.7 - - - +
251A SER* 1.3 67.3 + - - +
264A GLY 4.1 0.3 - - - +
265A ARG* 3.2 2.6 - - - -
266A GLN 2.9 31.6 + - - +
268A PRO* 4.0 11.4 - - + -
291A ALA* 5.8 1.6 - - + -
292A ARG 3.5 4.9 - - - +
293A CYS* 3.7 18.2 - - - -
316A ASN 4.3 8.5 - - - +
317A LEU* 4.4 13.2 - - + -
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 4.2 6.9 - - - +
250A VAL* 1.3 76.7 - - - +
252A GLY* 1.3 59.0 + - - +
253A TYR* 3.6 26.2 - - - -
264A GLY 3.3 6.5 - - - -
265A ARG* 3.3 21.5 + - - +
291A ALA* 3.1 7.4 - - - +
292A ARG 2.9 33.8 + - - -
317A LEU* 4.5 3.8 - - - -
350A ALA* 3.8 23.9 + - - -
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Residues in contact with GLY 252 (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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207A MET* 5.7 0.2 - - - -
251A SER* 1.3 73.6 - - - +
253A TYR* 1.3 66.9 + - - -
262A LEU* 3.9 2.1 - - - +
263A ILE* 2.9 29.1 + - - -
264A GLY 2.9 14.0 + - - +
290A ALA 3.3 8.1 - - - -
317A LEU* 3.5 24.8 - - - +
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Residues in contact with TYR 253 (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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207A MET* 5.7 0.5 - - - +
251A SER* 3.6 25.2 - - - -
252A GLY* 1.3 74.8 - - - -
254A ARG* 1.3 64.5 + - - +
255A VAL* 4.7 0.7 - - + -
260A TRP* 3.5 41.7 - + + -
261A THR 3.2 8.3 - - - +
262A LEU* 3.5 35.8 - - + +
263A ILE* 3.7 7.7 - - - +
265A ARG* 4.8 0.2 - - - -
289A LEU* 3.6 7.3 - - - +
290A ALA 2.7 39.5 + - - +
346A ILE* 4.2 18.4 - - + -
347A PRO* 3.7 17.7 - - + +
349A GLU* 2.7 42.0 + - - +
350A ALA* 3.8 8.6 - - + +
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Residues in contact with ARG 254 (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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253A TYR* 1.3 72.8 - - - +
255A VAL* 1.3 63.9 + - - +
256A ARG* 3.6 31.1 + - - +
259A GLN* 3.4 13.7 - - - +
260A TRP* 3.6 1.2 - - - -
261A THR* 2.8 70.6 + - - +
263A ILE* 3.7 4.4 - - + +
281A VAL* 3.8 17.5 - - + +
282A ASP* 2.8 49.8 + - - +
283A VAL* 4.2 15.9 - - + -
287A ASP* 3.3 32.1 - - + +
288A ILE 3.7 4.0 - - - +
289A LEU* 4.6 2.0 - - - -
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Residues in contact with VAL 255 (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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253A TYR* 4.7 0.4 - - + -
254A ARG* 1.3 77.6 - - - +
256A ARG* 1.3 60.4 + - - +
258A GLY* 4.0 15.9 - - - -
259A GLN 3.3 7.2 - - - +
260A TRP* 3.8 41.3 - - + +
287A ASP* 3.6 3.3 - - - -
288A ILE* 2.7 45.6 + - + +
290A ALA* 4.1 9.2 - - + -
342A MET* 3.8 28.7 - - + -
407A GOL 3.4 24.0 - - - +
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Residues in contact with ARG 256 (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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254A ARG* 3.6 31.4 + - - +
255A VAL* 1.3 73.6 - - - +
257A ASN* 1.3 84.2 + - + +
258A GLY 3.2 0.4 - - - -
259A GLN* 2.9 38.6 + - - +
282A ASP* 2.9 34.2 + - - -
284A THR* 3.2 15.2 + - - +
287A ASP* 2.7 40.6 + - - +
407A GOL 3.4 7.9 - - - +
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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