Contacts of the helix formed by residues 303 - 313 (chain A) in PDB entry 1PH3
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.6 18.7 + - - +
204A SER 5.3 1.0 + - - -
299A PHE* 3.5 30.8 - - - +
300A ILE 2.8 23.7 + - - -
301A GLN 3.1 4.0 + - - +
302A SER* 1.3 70.7 + - - +
304A LYS* 1.3 63.8 + - - +
305A LEU* 3.6 4.3 + - - +
306A ALA* 3.1 23.9 + - - +
307A LYS* 3.1 23.0 + - - +
310A ARG* 5.2 0.3 + - - -
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Residues in contact with LYS 304 (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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200A PHE 2.8 20.0 + - - +
201A SER* 3.5 22.9 - - - +
202A SER* 4.0 19.7 + - - +
203A TYR* 4.0 8.7 - - - +
204A SER* 5.1 6.8 + - - +
302A SER 3.1 2.6 + - - -
303A SER* 1.3 69.7 - - - +
305A LEU* 1.3 67.1 + - - +
307A LYS* 3.4 6.3 + - - +
308A GLU* 3.0 60.4 + - + +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE 4.7 0.2 + - - -
204A SER* 3.7 36.3 - - - +
206A ILE* 3.5 34.8 - - + +
211A TYR* 4.8 10.5 - - - +
227A VAL* 4.4 11.0 - - + -
270A VAL* 5.9 0.2 - - + -
299A PHE* 4.2 15.3 - - + -
303A SER* 3.4 4.9 + - - +
304A LYS* 1.3 82.3 - - - +
306A ALA* 1.3 62.1 + - - +
308A GLU* 3.5 10.1 + - - +
309A LEU* 3.1 50.6 + - + +
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Residues in contact with ALA 306 (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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270A VAL* 3.9 17.6 - - + +
299A PHE* 3.8 22.9 - - + +
300A ILE 5.2 0.4 - - - +
303A SER* 3.1 27.5 + - - +
305A LEU* 1.3 75.5 - - - +
307A LYS* 1.3 61.6 + - - +
309A LEU 3.5 0.2 + - - -
310A ARG* 3.0 51.7 + - - +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 5.6 3.6 - - - +
303A SER 3.1 18.8 + - - +
304A LYS* 3.7 6.7 - - - +
305A LEU 3.3 0.2 - - - -
306A ALA* 1.3 76.9 - - - +
308A GLU* 1.3 64.7 + - + +
310A ARG* 3.4 32.5 + - - +
311A ALA* 3.4 14.0 + - - +
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Residues in contact with GLU 308 (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 SER* 5.3 2.9 + - - -
304A LYS* 3.0 52.1 + - + +
305A LEU* 4.1 10.8 - - - +
307A LYS* 1.3 76.9 - - + +
309A LEU* 1.3 64.0 + - + +
311A ALA* 3.4 3.8 + - - +
312A LYS* 2.8 34.1 + - + +
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Residues in contact with LEU 309 (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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211A TYR* 5.8 0.9 - - - +
227A VAL* 3.7 34.5 - - + +
229A LYS* 4.3 1.2 - - - +
248A ALA* 5.0 11.2 - - + +
270A VAL* 3.7 22.9 - - + -
305A LEU* 3.1 38.9 + - + +
308A GLU* 1.3 81.6 - - + +
310A ARG* 1.3 65.4 + - - +
312A LYS* 4.4 18.8 - - + +
313A ILE* 3.0 47.6 + - + +
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Residues in contact with ARG 310 (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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229A LYS* 2.6 30.5 + - - +
268A GLY 3.6 23.6 - - - +
269A GLU* 4.4 22.9 + - - +
270A VAL* 3.7 13.7 - - + +
299A PHE 6.0 0.4 + - - -
301A GLN* 4.8 18.8 + - - +
303A SER 5.2 0.2 + - - -
306A ALA* 3.0 49.9 + - - +
307A LYS* 3.7 28.2 - - - +
309A LEU* 1.3 76.7 - - - +
311A ALA* 1.3 59.4 + - - +
313A ILE 3.7 0.3 - - - +
314A GLN* 4.0 2.8 + - - -
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Residues in contact with ALA 311 (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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307A LYS 3.4 12.3 + - - +
308A GLU* 4.0 4.3 - - - +
309A LEU 3.2 0.2 - - - -
310A ARG* 1.3 80.0 - - - +
312A LYS* 1.3 61.1 + - - +
314A GLN* 2.8 25.4 + - - +
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Residues in contact with LYS 312 (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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248A ALA* 4.3 29.2 + - + +
308A GLU* 2.8 25.3 + - + +
309A LEU* 4.4 15.6 - - + +
311A ALA* 1.3 76.8 - - - +
313A ILE* 1.3 65.7 + - + +
314A GLN* 3.3 8.5 + - - +
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Residues in contact with ILE 313 (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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228A ALA* 4.8 0.2 - - - -
229A LYS* 3.0 52.7 + - + +
231A LEU* 4.3 2.9 - - + -
246A LYS* 3.3 51.4 - - + +
247A ASP* 3.6 25.1 - - - +
248A ALA* 3.8 7.4 - - - +
309A LEU* 3.0 37.4 + - + +
310A ARG 3.7 0.3 - - - +
312A LYS* 1.3 77.5 - - + +
314A GLN* 1.3 66.9 + - - +
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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