Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 2HD5
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 ASP 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 4.2 2.2 - - - -
288A PHE* 4.9 0.5 - - - -
294A GLN* 1.3 74.9 + - - +
296A ALA* 1.3 60.1 + - - +
297A GLN* 2.8 31.8 + - - +
298A GLU* 2.9 23.0 + - + +
299A PHE* 3.0 27.7 + - - +
465A TYR* 3.6 3.6 - - - -
514A TYR* 2.6 28.0 + - - -
42B ARG* 3.4 10.1 + - - -
72B ARG* 3.4 26.2 - - + +
73B LEU 2.7 22.0 + - - +
74B ARG* 4.2 2.2 - - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 4.0 9.9 - - - +
228A ILE* 3.5 24.6 - - + +
294A GLN 3.9 0.6 + - - -
295A ASP* 1.3 73.0 + - - +
297A GLN* 1.3 58.8 + - - +
299A PHE* 3.3 7.0 + - - +
300A LEU* 2.8 28.4 + - - +
454A SER* 3.9 9.0 - - - +
465A TYR* 3.0 40.0 + - + -
514A TYR* 4.9 0.7 - - + -
515A LEU* 4.1 5.2 - - + -
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 2.8 15.6 + - - +
296A ALA* 1.3 71.6 - - - +
298A GLU* 1.3 58.5 + - - +
300A LEU* 3.2 4.5 + - + +
301A ARG* 2.9 45.4 + - - +
349A ASP* 2.8 28.1 + - - +
351A SER* 4.0 4.0 + - - -
405A HIS* 3.4 43.1 + - + +
514A TYR* 4.4 1.7 - - + +
515A LEU* 3.8 21.6 - - + +
42B ARG* 2.7 37.1 + - - -
44B ILE* 4.3 8.5 - - - +
70B VAL* 4.1 2.1 - - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 3.6 22.4 + - - -
288A PHE* 4.4 7.7 - - + -
294A GLN* 4.7 2.6 - - - +
295A ASP* 2.9 19.5 + - + +
297A GLN* 1.3 78.1 - - - +
299A PHE* 1.3 61.1 + - - +
301A ARG* 3.3 2.2 + - - +
302A PHE* 3.1 45.1 + - + -
42B ARG* 3.5 24.4 - - - +
49B GLN* 2.8 33.8 + - - +
72B ARG* 2.8 37.6 + - - +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 3.8 23.3 - + + -
225A MET* 3.5 52.0 - - + -
228A ILE* 3.7 23.8 - - + -
229A LEU* 4.6 1.8 - - + -
279A PHE* 3.7 20.6 - + - -
283A ILE* 3.9 24.2 - - + -
288A PHE* 3.6 25.1 - + + -
295A ASP 3.0 14.4 + - - +
296A ALA 3.4 6.7 - - - +
297A GLN 3.2 0.2 - - - -
298A GLU* 1.3 72.9 - - - +
300A LEU* 1.3 65.2 + - - +
302A PHE* 3.3 1.6 + - - +
303A LEU* 2.9 44.0 + - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 3.8 30.3 - - + -
232A LEU* 4.2 15.5 - - + -
296A ALA 2.8 15.5 + - - +
297A GLN* 3.2 6.0 + - + +
299A PHE* 1.3 77.4 - - - +
301A ARG* 1.3 77.5 + - - +
303A LEU* 3.8 1.7 - - + +
304A LEU* 2.9 60.8 + - + +
349A ASP* 4.8 0.9 - - - +
403A VAL* 4.0 25.6 - - + -
515A LEU* 4.5 11.4 - - + -
517A PHE* 4.3 15.0 - - + -
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Residues in contact with ARG 301 (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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297A GLN* 2.9 39.4 + - - +
298A GLU* 3.7 6.7 - - - +
300A LEU* 1.3 96.5 - - - +
302A PHE* 1.3 63.0 + - - +
304A LEU* 3.6 33.8 - - - +
305A ASP* 3.1 25.6 + - - +
348A TRP* 3.3 30.6 + - - +
349A ASP* 2.9 42.1 + - - +
403A VAL* 5.4 0.4 - - - +
44B ILE* 3.9 24.0 - - + -
47B GLY* 2.8 31.2 + - - +
48B LYS* 5.8 0.2 - - - -
49B GLN* 4.8 15.3 - - + +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.2 7.2 - - + +
284A TYR* 4.8 10.3 - - + +
285A ALA* 3.8 28.9 - - + -
287A ARG* 6.1 3.1 - - + -
288A PHE* 4.2 12.3 - + + -
298A GLU* 3.1 52.6 + - + +
299A PHE 4.1 1.6 - - - +
301A ARG* 1.3 76.2 - - - +
303A LEU* 1.3 57.9 + - - +
305A ASP* 3.5 9.5 + - + +
306A GLY* 3.0 26.3 + - - -
49B GLN* 3.6 39.3 - - + -
51B GLU* 3.8 35.4 - - + -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 4.5 1.1 - - + -
229A LEU* 4.0 13.2 - - + -
232A LEU* 3.5 30.5 - - + -
256A LEU* 4.2 4.9 - - + -
260A PHE* 4.3 3.6 - - + -
279A PHE* 3.6 27.4 - - + -
283A ILE* 3.7 17.6 - - + +
299A PHE* 2.9 44.2 + - + +
300A LEU* 3.8 3.4 - - - +
302A PHE* 1.3 78.2 - - - +
304A LEU* 1.3 58.6 + - + +
306A GLY* 3.3 1.7 + - - -
307A LEU* 2.9 53.7 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.3 16.6 - - + -
238A LEU* 4.9 2.7 - - + -
300A LEU* 2.9 44.1 + - + +
301A ARG* 3.6 25.6 - - - +
303A LEU* 1.3 73.6 - - + +
305A ASP* 1.3 56.9 + - - +
307A LEU* 3.4 21.5 + - + +
308A HIS* 2.8 33.6 + - - +
320A ILE* 4.1 14.3 - - + +
324A PHE* 4.0 39.0 - - + -
348A TRP* 4.2 10.3 - - + -
403A VAL* 5.7 0.2 - - + -
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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 ARG* 3.1 20.1 + - - +
302A PHE* 3.7 10.8 - - + +
304A LEU* 1.3 76.9 - - - +
306A GLY* 1.3 54.9 + - - +
308A HIS* 3.6 10.1 - - - +
309A ASN* 2.7 58.3 + - - -
348A TRP* 5.2 3.3 - - - -
47B GLY 5.2 3.8 - - - +
48B LYS* 3.9 37.8 - - + +
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Residues in contact with GLY 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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256A LEU* 3.6 22.2 - - - -
284A TYR* 4.1 21.8 - - - -
302A PHE 3.0 14.8 + - - -
303A LEU 3.7 0.4 - - - -
305A ASP* 1.3 73.2 - - - +
307A LEU* 1.3 64.7 + - - +
309A ASN* 3.3 2.7 + - - +
310A GLU* 3.0 28.1 + - - +
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Residues in contact with LEU 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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238A LEU* 5.2 1.3 - - + -
256A LEU* 3.8 9.5 - - + +
257A VAL* 3.7 36.6 - - + +
260A PHE* 3.8 42.6 - - + -
303A LEU* 2.9 32.6 + - + +
304A LEU* 3.7 23.3 - - + +
306A GLY* 1.3 73.2 - - - +
308A HIS* 1.3 64.3 + - - +
310A GLU* 3.0 15.6 + - - +
311A VAL* 3.2 16.5 + - - +
320A ILE* 4.1 22.2 - - + -
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Residues in contact with HIS 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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304A LEU 2.8 18.0 + - - +
305A ASP* 3.6 10.3 - - - +
307A LEU* 1.3 77.9 - - - +
309A ASN* 1.3 72.0 + - - +
311A VAL 3.2 2.3 + - - -
312A ASN* 2.9 34.1 + - - +
316A GLU* 2.6 38.7 + - + +
317A ASP 3.7 22.9 - - - -
318A SER* 2.6 36.5 + - - +
320A ILE* 4.0 5.8 - - + +
321A GLY* 5.0 1.1 - - - -
348A TRP* 3.5 33.8 - + + -
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Residues in contact with ASN 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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249A GLY* 3.2 2.6 - - - -
250A SER* 2.7 58.1 + - - +
251A ASN* 5.6 3.8 - - - +
284A TYR* 5.1 10.3 - - + +
305A ASP* 2.7 49.8 + - - +
306A GLY* 3.8 5.6 - - - +
307A LEU 3.3 0.2 - - - -
308A HIS* 1.3 87.5 - - - +
310A GLU* 1.3 61.9 + - + +
311A VAL 3.4 0.3 + - - -
312A ASN* 3.6 2.5 + - - -
316A GLU* 5.0 4.8 + - - +
48B LYS* 5.2 4.9 - - - +
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Residues in contact with GLU 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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245A ASP 5.4 3.3 - - - -
249A GLY* 3.7 13.6 + - - -
250A SER 4.9 0.4 - - - +
251A ASN* 4.8 1.8 - - - +
253A HIS* 3.4 24.1 - - - +
254A THR* 3.1 22.0 - - - +
256A LEU* 3.3 9.8 - - - +
257A VAL* 2.8 36.3 + - + +
283A ARG* 2.6 31.2 - - - -
284A TYR* 2.6 27.9 + - - +
306A GLY 3.0 11.8 + - - +
307A LEU 3.0 6.4 + - - +
309A ASN* 1.3 79.1 - - - +
311A VAL* 1.3 61.6 + - - +
312A ASN 3.6 0.2 - - - -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.7 25.6 - - + +
244A TYR* 4.3 9.4 - - - +
245A ASP* 4.0 27.3 - - + +
249A GLY 4.3 1.3 - - - +
257A VAL* 4.1 27.1 - - + -
307A LEU 3.2 15.2 + - - +
308A HIS 3.5 3.1 - - - +
310A GLU* 1.3 81.4 - - - +
312A ASN* 1.3 66.4 + - - +
313A ARG* 3.1 7.1 + - - +
318A SER* 3.6 12.9 - - - -
319A ARG 4.8 1.5 + - - +
320A ILE* 4.0 22.0 - - + -
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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
------------------------------------------------------------
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