Contacts of the strand formed by residues 242 - 249 (chain A) in PDB entry 4FQP
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 TYR 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.5 16.2 - - + -
212A SER* 3.6 43.9 + - - -
215A ASP* 3.9 10.3 + - + +
240A VAL* 3.3 22.0 - - + -
241A TYR* 1.3 74.6 - - - +
243A PRO* 1.3 94.4 - - + +
245A GLU* 4.3 5.2 - - - -
269A ARG* 3.1 55.8 + - - +
270A SER* 3.6 11.1 + - - -
271A ASN* 2.9 40.5 + - + +
316A ASN* 3.6 6.4 + - - -
318A LEU* 3.9 9.8 - - - +
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Residues in contact with PRO 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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156A LEU* 3.7 15.7 - - + -
242A TYR* 1.3 110.5 - - + +
244A PRO* 1.3 78.0 - - + +
245A GLU* 3.4 3.5 + - - +
316A ASN* 3.9 4.5 - - - +
318A LEU* 4.3 15.0 - - + -
319A GLY 4.9 5.2 - - - +
321A ARG* 3.7 39.5 - - + +
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Residues in contact with PRO 244 (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 PRO* 1.3 86.9 - - + +
245A GLU* 1.3 61.5 + - - +
246A VAL* 3.9 10.5 + - + -
268A ALA* 4.8 3.1 - - + -
270A SER* 3.6 15.7 - - - -
314A VAL* 3.7 39.3 - - + +
316A ASN* 3.3 34.5 - - + +
319A GLY 4.0 8.7 - - - +
321A ARG* 3.1 32.8 - - + +
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Residues in contact with GLU 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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212A SER* 2.7 31.0 + - - -
242A TYR* 4.3 2.6 - - - -
243A PRO 4.2 6.1 - - - +
244A PRO* 1.3 73.5 - - - +
246A VAL* 1.3 60.7 + - - +
267A ASP 4.1 0.3 - - - +
268A ALA* 3.3 3.8 - - - -
269A ARG* 2.5 71.5 + - + +
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Residues in contact with VAL 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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244A PRO* 4.0 16.6 - - + +
245A GLU* 1.3 77.5 - - - +
247A SER* 1.3 67.5 + - - +
266A CYS* 3.4 32.5 - - - -
267A ASP 3.6 5.4 - - - +
268A ALA* 4.2 1.6 - - + -
312A CYS* 4.1 5.4 - - + +
314A VAL* 3.7 28.5 - - + -
321A ARG* 4.2 16.5 - - + +
322A GLN 4.2 3.7 + - - +
323A ALA* 3.1 30.2 - - + +
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Residues in contact with SER 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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245A GLU 4.2 0.4 + - - -
246A VAL* 1.3 77.4 - - - +
248A ILE* 1.3 65.6 + - - +
249A SER* 4.2 0.4 - - - -
266A CYS* 3.6 2.6 - - - -
267A ASP* 2.8 47.2 + - - +
323A ALA* 3.9 7.2 - - - -
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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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247A SER* 1.3 81.1 - - - +
249A SER* 1.3 61.0 + - - +
264A LEU* 4.1 15.5 - - + -
265A THR 3.2 16.4 - - - +
266A CYS* 5.0 0.7 - - - -
267A ASP* 4.3 0.4 - - - -
279A TRP* 3.9 23.8 - - + -
310A LEU* 4.1 9.4 - - + +
312A CYS* 4.4 17.7 - - + -
323A ALA* 3.7 29.8 - - + +
324A GLU 4.0 5.7 + - - +
325A LEU* 3.8 47.0 - - + +
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Residues in contact with SER 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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247A SER* 5.8 0.2 - - - -
248A ILE* 1.3 74.1 - - - +
250A GLY* 1.3 61.1 + - - +
251A TYR* 3.8 1.1 - - - +
264A LEU* 3.3 7.4 - - - +
265A THR* 3.0 34.2 + - - +
267A ASP* 2.9 30.8 + - - -
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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