Contacts of the helix formed by residues 245 - 254 (chain A) in PDB entry 1P4F
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 SER 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A GLU* 2.7 34.9 + - - -
243A ASN 3.7 1.6 + - - -
244A THR* 1.3 76.6 - - - +
246A ALA* 1.3 63.8 + - - +
247A LEU* 3.7 7.8 + - - +
248A ALA* 3.1 18.5 + - - +
249A LYS* 3.3 20.0 + - - +
274A TRP* 3.9 3.5 + - - -
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Residues in contact with ALA 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 THR 3.7 1.0 + - - -
245A SER* 1.3 73.7 - - - +
247A LEU* 1.3 57.3 + - - +
249A LYS* 3.2 13.7 + - + +
250A ASP* 2.8 29.6 + - - +
253A ARG* 4.9 2.6 + - - +
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Residues in contact with LEU 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 SER* 3.2 8.7 + - - +
246A ALA* 1.3 75.3 - - - +
248A ALA* 1.3 60.0 + - - +
250A ASP* 4.0 8.5 - - + -
251A PHE* 2.9 26.2 + - - +
272A HIS* 3.5 32.6 - - + +
273A PRO* 3.8 40.4 - - + +
274A TRP* 4.1 14.4 - - + +
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Residues in contact with ALA 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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113A GLU* 3.9 2.0 - - - +
211A LEU* 3.7 15.9 - - + +
244A THR* 3.8 9.4 - - + -
245A SER* 3.1 21.4 + - - +
247A LEU* 1.3 75.6 - - - +
249A LYS* 1.3 63.0 + - - +
251A PHE* 3.3 5.4 + - - +
252A ILE* 3.1 27.5 + - - +
274A TRP* 3.5 39.2 - - + -
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Residues in contact with LYS 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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236A PHE* 3.5 44.4 + - + +
238A ASP* 4.9 9.1 + - - -
241A PHE* 3.7 45.7 + - + +
244A THR* 4.1 13.1 + - + -
245A SER 3.3 9.3 + - - +
246A ALA* 3.2 13.2 + - - +
248A ALA* 1.3 73.7 - - - +
250A ASP* 1.3 61.1 + - - +
252A ILE* 3.3 2.2 + - - -
253A ARG* 2.8 48.9 + - - +
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Residues in contact with ASP 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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246A ALA 2.8 16.8 + - - +
247A LEU* 3.5 16.6 - - + +
249A LYS* 1.3 76.1 - - - +
251A PHE* 1.3 61.8 + - - +
253A ARG* 3.4 12.4 + - - +
254A ARG* 2.7 67.1 + - - +
272A HIS* 2.8 21.9 + - + +
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Residues in contact with PHE 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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120A LEU* 3.6 27.8 - - + -
124A LEU* 4.2 9.2 - - + -
203A ILE* 4.7 1.1 - - + -
207A THR* 3.8 13.9 - - + -
247A LEU 2.9 12.9 + - - +
248A ALA 3.3 9.0 - - - +
250A ASP* 1.3 77.4 - - - +
252A ILE* 1.3 63.6 + - - +
254A ARG 3.4 6.1 + - - -
255A LEU* 3.5 37.2 - - + +
264A MET* 3.5 10.9 - - + +
269A SER* 3.7 28.7 - - - -
272A HIS* 3.4 32.6 + + + -
274A TRP* 3.6 24.0 - + + -
275A ILE* 3.5 20.9 - - + -
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Residues in contact with ILE 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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204A GLY 4.0 9.6 - - - +
207A THR* 3.7 23.1 - - + -
208A TYR* 3.8 27.8 - - + +
211A LEU* 3.9 19.1 - - + -
236A PHE* 3.8 28.7 - - + -
241A PHE* 4.4 6.1 - - + -
248A ALA 3.1 17.7 + - - +
249A LYS* 3.3 5.8 + - - +
251A PHE* 1.3 76.9 - - - +
253A ARG* 1.3 64.2 + - - +
255A LEU* 3.0 9.6 + - - +
256A LEU* 3.0 44.4 + - + +
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Residues in contact with ARG 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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234A TYR* 3.6 18.2 - - - +
235A GLU* 4.7 4.2 + - - -
236A PHE* 3.4 32.1 - - + -
246A ALA* 4.9 3.0 + - - +
249A LYS* 2.8 42.2 + - - +
250A ASP* 3.8 11.8 - - - +
252A ILE* 1.3 73.2 - - - +
254A ARG* 1.3 61.6 + - + +
255A LEU 3.2 0.9 + - - -
256A LEU 3.6 8.1 + - - +
257A VAL* 3.3 16.1 - - - +
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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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250A ASP* 2.7 50.5 + - - +
251A PHE 3.9 4.0 - - - +
252A ILE 3.2 1.0 - - - -
253A ARG* 1.3 77.5 - - + +
255A LEU* 1.3 58.6 + - - +
257A VAL* 3.6 15.0 - - - +
262A LYS 4.5 1.2 - - - +
263A ARG* 3.7 1.0 - - - -
264A MET* 3.1 52.3 + - + -
272A HIS* 4.3 5.1 + - - -
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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