Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 1PHP
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 GLY 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.1 31.8 + - - -
266A VAL* 3.7 5.8 - - - +
267A VAL* 4.4 4.3 - - - -
295A ILE* 1.3 71.4 - - - +
297A PRO* 1.3 73.3 - - - +
299A THR* 3.2 1.9 + - - -
300A ARG* 2.9 36.6 + - - +
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Residues in contact with PRO 297 (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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265A ASP* 3.2 11.2 - - - +
280A VAL* 3.8 27.4 - - + -
296A GLY* 1.3 82.3 - - - +
298A LYS* 1.3 67.9 + - + +
300A ARG* 3.3 27.4 + - - +
301A GLU* 3.2 21.0 + - - +
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Residues in contact with LYS 298 (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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264A VAL* 3.9 16.6 - - + +
265A ASP* 2.9 27.9 + - + +
297A PRO* 1.3 77.0 - - + +
299A THR* 1.3 58.8 + - - +
301A GLU* 3.3 10.6 + - - +
302A LEU* 3.0 27.9 + - - +
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Residues in contact with THR 299 (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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262A MET 4.8 0.2 - - - +
263A PRO* 3.6 11.7 - - + -
264A VAL* 2.9 24.5 + - - +
265A ASP* 2.7 25.8 + - - -
295A ILE* 3.9 17.3 - - + -
296A GLY 3.6 5.2 - - - -
298A LYS* 1.3 73.6 - - - +
300A ARG* 1.3 67.9 + - - +
302A LEU* 3.2 5.6 + - + -
303A TYR* 2.9 67.1 + - + +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A VAL* 3.7 19.8 - - - +
294A ASP* 3.8 8.7 + - - -
295A ILE* 2.9 46.3 + - + -
296A GLY* 2.9 22.1 + - - +
297A PRO* 3.3 20.3 + - - +
299A THR* 1.3 78.1 - - - +
301A GLU* 1.3 55.4 + - - +
303A TYR* 3.4 3.4 + - - +
304A ARG* 2.9 30.7 + - - +
329A HIS* 3.7 27.2 - - - +
330A GLY* 3.7 6.7 - - - -
333A ALA* 3.9 31.1 - - + +
334A ILE* 5.0 3.6 - - - +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO 3.2 9.7 + - - +
298A LYS* 3.6 12.6 - - - +
299A THR 3.1 0.4 - - - -
300A ARG* 1.3 76.9 - - - +
302A LEU* 1.3 63.6 + - - +
304A ARG* 3.4 17.6 + - - +
305A ASP* 3.1 40.5 + - - +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.9 33.4 - - + -
262A MET 4.5 4.7 - - - +
264A VAL* 4.5 22.7 - - + -
298A LYS 3.0 16.3 + - - +
299A THR* 3.6 6.5 - - - +
301A GLU* 1.3 73.2 - - - +
303A TYR* 1.3 88.3 - - + +
305A ASP* 3.2 12.2 + - + +
306A VAL* 3.1 22.9 + - + +
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Residues in contact with TYR 303 (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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192A ILE* 6.0 0.2 - - + -
216A ILE* 3.3 45.2 - - + +
217A ILE 2.7 23.7 + - - -
261A TYR* 4.0 12.1 + + + -
262A MET* 3.1 6.5 - - - -
263A PRO* 3.1 20.8 - - - +
295A ILE* 4.0 14.6 - - + -
299A THR* 2.9 40.1 + - + +
300A ARG 3.9 1.1 - - - +
302A LEU* 1.3 94.4 - - + +
304A ARG* 1.3 68.1 + - - +
306A VAL* 3.2 4.3 + - + +
307A ILE* 3.0 28.7 + - + +
319A MET* 4.1 14.4 - - - -
334A ILE* 3.8 22.9 - - + -
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Residues in contact with ARG 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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300A ARG 2.9 18.5 + - - +
301A GLU* 3.6 16.2 + - - +
302A LEU 3.2 0.2 - - - -
303A TYR* 1.3 76.7 - - - +
305A ASP* 1.3 58.6 + - - +
307A ILE* 3.3 2.8 + - - +
308A ARG* 2.9 53.7 + - - +
333A ALA 5.5 2.2 + - - +
334A ILE* 5.2 1.6 - - + +
336A GLU* 5.9 0.8 + - - -
337A ALA* 3.8 30.8 - - + +
340A GLU* 3.8 18.6 + - - +
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Residues in contact with ASP 305 (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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301A GLU* 3.1 32.6 + - - +
302A LEU* 3.5 12.7 - - + +
304A ARG* 1.3 77.1 - - - +
306A VAL* 1.3 63.6 + - + +
308A ARG* 3.1 26.8 + - - +
309A GLU* 3.3 36.4 + - - +
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Residues in contact with VAL 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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190A THR* 4.0 6.5 - - + +
214A ASN* 4.0 30.2 + - + +
216A ILE* 3.9 22.0 - - + -
261A TYR* 3.7 38.6 - - + +
302A LEU* 3.1 21.0 + - + +
303A TYR* 3.2 6.2 + - + +
305A ASP* 1.3 73.5 - - + +
307A ILE* 1.3 59.8 + - - +
309A GLU* 3.1 16.2 + - - +
310A SER* 2.8 24.3 + - - -
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Residues in contact with ILE 307 (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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190A THR* 5.5 1.6 - - + -
192A ILE* 3.7 32.3 - - + -
216A ILE* 5.0 4.0 - - + -
303A TYR 3.0 21.0 + - - +
304A ARG* 3.5 7.6 - - - +
306A VAL* 1.3 74.7 - - - +
308A ARG* 1.3 58.5 + - + +
310A SER* 2.9 26.5 + - - -
313A VAL* 4.6 8.1 - - + -
334A ILE* 4.0 20.4 - - + +
337A ALA* 3.9 37.9 - - + +
338A LEU* 3.7 25.1 - - + -
341A ALA* 4.3 9.0 - - + -
344A THR* 3.4 12.0 + - + +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 2.9 26.2 + - - +
305A ASP* 3.1 39.8 + - - +
306A VAL 3.2 0.4 - - - -
307A ILE* 1.3 76.7 - - + +
309A GLU* 1.3 59.1 + - + +
310A SER 3.7 1.4 + - - +
311A LYS* 5.1 2.9 + - - -
340A GLU* 2.9 36.6 + - - +
341A ALA* 4.4 11.6 - - + +
344A THR* 4.3 9.1 + - - -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 3.4 23.8 - - + +
214A ASN* 6.2 0.2 - - - -
305A ASP* 3.3 26.0 - - - +
306A VAL* 3.1 11.1 + - - +
308A ARG* 1.3 79.0 - - + +
310A SER* 1.3 60.3 + - - +
311A LYS* 3.8 11.1 + - - +
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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