Contacts of the strand formed by residues 247 - 252 (chain A) in PDB entry 1P4A
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 MET 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.6 15.9 - - + -
122A PHE* 3.2 42.8 - - + -
125A VAL* 3.9 32.3 - - + -
126A PHE* 4.4 7.0 - - + -
229A ILE 2.7 14.9 + - - +
230A GLY* 3.5 0.3 - - - -
231A VAL* 2.8 28.8 + - - +
246A TYR* 1.3 76.5 - - - +
248A SER* 1.3 65.8 + - - +
249A LEU* 3.9 2.0 - - + -
268A ASN* 3.3 3.6 - - - -
269A PHE* 3.8 24.9 - - + -
272A PHE* 3.3 30.2 - - + -
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Residues in contact with SER 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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231A VAL* 3.3 23.3 - - - -
234A GLU* 2.9 33.9 + - - -
246A TYR* 4.0 5.4 - - - -
247A MET* 1.3 74.5 - - - +
249A LEU* 1.3 64.0 + - - +
250A LEU 4.3 4.3 - - - -
267A GLY* 3.4 4.0 - - - -
268A ASN* 2.8 24.9 + - - -
269A PHE* 3.1 24.1 + - - +
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Residues in contact with LEU 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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83A PHE* 4.8 3.4 - - + -
84A VAL* 3.5 30.2 - - + +
87A LEU* 5.1 1.1 - - + -
118A VAL* 3.9 23.3 - - + -
121A LEU* 3.7 43.1 - - + -
122A PHE* 4.1 4.7 - - + -
231A VAL 3.3 9.7 + - - +
232A LEU* 3.4 33.0 + - + +
247A MET* 3.9 10.8 - - + -
248A SER* 1.3 75.2 - - - +
250A LEU* 1.3 58.7 - - + +
267A GLY* 2.6 23.4 + - - -
269A PHE* 3.7 21.7 - - + -
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Residues in contact with LEU 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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84A VAL* 3.7 33.9 - - + +
87A LEU* 3.9 23.3 - - + -
88A GLY* 3.7 30.7 - - - +
91A LEU* 3.9 19.1 - - + -
232A LEU 3.0 10.5 + - - +
233A VAL* 3.4 14.2 - - + -
234A GLU* 2.9 28.0 + - - +
248A SER* 4.3 2.1 - - - -
249A LEU* 1.3 81.3 - - + +
251A THR* 1.3 63.7 + - - +
264A ILE* 4.0 9.4 - - + -
265A GLN 3.4 13.0 - - - +
266A ASN* 4.3 5.6 - - - +
267A GLY* 4.0 1.6 - - - -
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Residues in contact with THR 251 (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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233A VAL* 4.7 1.3 - - - -
234A GLU* 3.2 27.5 + - + +
236A GLU* 4.2 33.7 - - + +
250A LEU* 1.3 76.8 + - - +
252A LEU* 1.3 63.5 + - - +
253A SER* 5.9 1.1 - - - -
263A GLU 3.8 0.5 - - - +
264A ILE* 3.3 9.4 - - - +
265A GLN* 2.7 47.8 + - + +
266A ASN 3.3 16.2 + - - -
267A GLY* 3.5 7.3 - - - -
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Residues in contact with LEU 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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91A LEU* 4.8 5.8 - - + -
103A VAL* 3.7 22.2 - - + -
105A LEU* 5.5 0.9 - - + -
205A PHE* 3.6 27.4 - - + -
233A VAL* 3.9 19.0 - - + +
234A GLU 2.7 11.7 + - - +
235A ALA* 3.5 8.3 - - + +
236A GLU 3.0 23.7 + - - -
250A LEU 4.3 0.2 - - - -
251A THR* 1.3 74.8 - - - +
253A SER* 1.3 62.6 + - - +
255A ILE* 3.6 27.8 - - + -
262A ILE* 3.3 29.8 - - + -
263A GLU 3.7 3.1 - - - -
264A ILE* 4.4 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