Contacts of the strand formed by residues 242 - 250 (chain A) in PDB entry 4EG8
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 PHE 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A LYS* 3.5 4.5 + - - -
241A VAL* 1.3 70.0 - - - +
243A PHE* 1.3 57.4 + - - +
244A VAL* 3.8 21.1 - - + -
269A ILE* 3.7 19.3 - - + -
273A HIS* 3.2 55.6 - + + -
278A GLU* 4.2 12.6 - - + +
279A ARG 2.8 18.4 + - - +
280A VAL* 3.4 9.6 - - + +
281A PHE 2.9 26.2 + - - +
511A ASP* 3.4 34.1 - - + -
512A VAL* 4.0 12.3 - - + -
657A LEU* 5.4 1.3 - - + -
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Residues in contact with PHE 243 (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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241A VAL 3.2 1.5 + - - +
242A PHE* 1.3 73.6 - - - +
244A VAL* 1.3 59.9 + - - +
245A THR* 3.4 25.4 - - + -
281A PHE* 3.4 35.2 - + - -
283A LEU* 4.1 13.5 - - + -
481A TYR* 3.5 29.6 - - + -
485A SER* 3.9 16.2 - - - -
507A ARG* 3.2 38.6 - - + +
508A PHE* 4.2 5.2 - + - -
509A PRO 3.8 0.2 - - - -
510A ALA* 3.5 27.8 - - + -
511A ASP* 2.7 40.4 + - - +
512A VAL 3.3 4.2 + - - -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.8 16.8 - - + -
243A PHE* 1.3 74.6 - - - +
245A THR* 1.3 70.5 + - - +
266A THR* 3.9 27.7 - - + +
269A ILE* 4.1 14.6 - - + -
270A GLY* 4.1 15.5 - - - +
280A VAL* 4.5 2.7 - - + -
281A PHE 3.2 5.5 + - - +
282A ALA* 3.2 23.0 - - + -
283A LEU 3.0 22.2 + - - -
512A VAL* 3.3 22.9 - - + +
514A VAL* 4.3 4.3 - - + -
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Residues in contact with THR 245 (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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243A PHE* 3.4 35.9 - - + -
244A VAL* 1.3 79.6 - - - +
246A SER* 1.3 59.2 + - - +
266A THR* 3.0 12.2 + - - -
283A LEU* 3.5 12.1 - - + -
481A TYR* 3.4 27.9 - - + -
510A ALA* 4.4 2.2 - - + -
512A VAL 3.0 4.6 + - - -
513A HIS* 2.7 34.5 + - + +
514A VAL* 2.9 26.0 + - - +
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Residues in contact with SER 246 (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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245A THR* 1.3 74.0 - - - +
247A PRO* 1.3 84.0 + - - +
248A ILE* 3.7 3.1 + - - +
249A TYR* 3.3 9.6 + - - -
262A SER 4.4 0.7 - - - -
263A THR* 4.1 5.4 - - - -
266A THR* 3.2 19.3 - - - -
283A LEU* 2.9 12.8 + - - +
284A THR* 2.7 31.7 + - - -
480A ASN* 5.2 0.2 - - - +
481A TYR* 3.3 20.2 - - - -
514A VAL 3.7 3.8 - - - -
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Residues in contact with PRO 247 (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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246A SER* 1.3 105.8 + - - +
248A ILE* 1.3 60.2 + - - +
249A TYR* 3.3 35.6 - - + +
262A SER* 3.9 13.5 - - - +
284A THR* 4.1 0.7 + - - -
481A TYR* 3.7 11.7 - - - +
514A VAL 3.2 16.9 - - - +
515A ILE* 4.0 13.9 - - + -
516A GLY 4.6 1.3 - - - +
519A ILE* 3.9 24.0 - - + -
815A MET* 3.8 9.2 - - + -
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Residues in contact with ILE 248 (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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246A SER 3.7 2.0 + - - +
247A PRO* 1.3 73.5 - - - +
249A TYR* 1.3 52.4 + - - +
284A THR* 4.3 2.0 - - - -
285A GLY 3.2 21.8 - - - +
286A THR 3.8 5.6 - - - +
287A ASP* 3.9 9.6 - - + -
330A ILE* 3.7 17.5 - - + -
332A THR* 3.2 35.0 - - + -
477A ALA* 3.6 20.4 - - - +
480A ASN* 3.4 35.4 - - + +
481A TYR* 4.6 0.4 + - - -
815A MET* 2.7 50.3 + - + +
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Residues in contact with TYR 249 (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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246A SER* 3.3 7.6 + - - -
247A PRO* 3.3 35.2 - - + -
248A ILE* 1.3 73.7 - - - +
250A TYR* 1.3 65.4 + - - +
251A VAL* 3.4 1.4 + - - +
258A GLY 4.8 0.4 - - - -
259A HIS* 3.2 40.2 + + + -
262A SER* 3.1 23.2 - - - -
263A THR* 2.6 30.1 + - - -
284A THR* 3.6 8.3 - - - -
285A GLY 2.9 17.1 + - - +
286A THR* 3.4 8.1 - - - -
287A ASP 2.8 19.9 + - - -
315A PHE* 3.6 31.6 - + + -
319A PHE* 3.8 9.4 - + - -
815A MET* 3.8 7.9 - - - +
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Residues in contact with TYR 250 (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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249A TYR* 1.3 73.8 - - - +
251A VAL* 1.3 58.4 + - - +
252A ASN* 3.2 24.1 + - - +
253A ALA 4.4 2.1 - - - +
259A HIS* 4.9 4.6 + - - -
287A ASP* 3.3 30.9 + - - -
289A HIS 4.9 1.8 - - - -
292A LYS* 3.8 27.8 - - + -
293A VAL* 4.4 8.7 - - + -
315A PHE* 3.9 14.2 - - - -
366A SER 4.4 7.4 - - - -
367A ASP* 3.8 4.8 + - - -
368A GLU* 3.4 27.0 - - + +
473A VAL* 4.3 10.0 - - + +
474A TRP* 3.2 31.6 + + - -
815A MET* 3.3 46.8 + - - +
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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