Contacts of the helix formed by residues 309 - 330 (chain A) in PDB entry 2HU2
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 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 2.9 32.6 + - - -
307A TRP 3.5 2.2 + - - -
308A TYR* 1.3 88.5 - - - +
310A GLU* 1.3 60.5 + - - +
311A GLN* 3.9 11.2 + - - -
312A ALA* 3.1 12.0 + - - +
313A SER* 2.8 28.8 + - - -
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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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308A TYR* 4.0 20.8 + - - +
309A SER* 1.3 71.3 - - - +
311A GLN* 1.3 67.3 + - + +
313A SER* 3.4 4.9 + - - -
314A ILE* 3.0 54.1 + - + +
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 5.1 2.9 - - - +
309A SER* 4.1 11.4 - - - +
310A GLU* 1.3 89.6 - - + +
312A ALA* 1.3 52.7 + - - +
314A ILE* 3.4 7.8 + - - +
315A GLU* 2.8 41.1 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 3.6 21.1 - - - +
113A SER* 4.0 6.1 - - - -
116A GLU* 3.5 15.8 + - - +
307A TRP* 3.9 13.7 - - + +
309A SER* 3.1 21.6 + - - +
311A GLN* 1.3 78.6 - - - +
313A SER* 1.3 58.7 + - - +
315A GLU* 3.5 4.7 - - - +
316A MET* 3.0 38.2 + - + +
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TRP* 4.1 19.2 - - - -
308A TYR* 4.0 18.6 - - - -
309A SER 2.8 16.2 + - - -
310A GLU* 3.6 6.1 - - - -
312A ALA* 1.3 76.3 - - - +
314A ILE* 1.3 61.8 + - - +
316A MET* 3.5 8.1 - - - +
317A ARG* 3.2 43.7 + - - +
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Residues in contact with ILE 314 (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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29A VAL* 4.1 24.9 - - + -
310A GLU* 3.0 43.8 + - + +
311A GLN* 3.9 5.8 - - - +
313A SER* 1.3 73.5 - - - +
315A GLU* 1.3 67.1 + - - +
317A ARG* 3.3 3.0 + - - +
318A GLU* 3.0 49.3 + - - +
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Residues in contact with GLU 315 (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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109A VAL* 5.4 0.2 - - - -
111A ALA 3.5 21.1 - - - +
112A ALA* 3.6 18.6 - - + +
311A GLN* 2.8 23.4 + - - +
312A ALA* 3.3 6.6 + - - +
314A ILE* 1.3 79.0 - - - +
316A MET* 1.3 60.3 + - - +
318A GLU* 3.5 7.8 + - - +
319A GLU* 3.2 23.8 + - + +
322A ARG* 4.7 2.1 + - - -
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Residues in contact with MET 316 (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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65A TYR* 5.7 0.9 - - - -
87A ILE* 3.9 14.9 - - + +
88A GLY* 4.1 23.3 - - - -
109A VAL* 3.6 33.3 - - + +
112A ALA* 3.7 11.9 - - + +
113A SER* 3.8 20.4 - - - +
307A TRP* 3.7 35.2 - - + -
312A ALA 3.0 26.1 + - - +
313A SER 3.5 8.3 - - - +
315A GLU* 1.3 74.7 - - - +
317A ARG* 1.3 63.4 + - + +
320A ALA* 2.9 30.8 + - - +
801A FMT 4.2 8.5 - - - +
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Residues in contact with ARG 317 (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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26A ASP* 3.0 47.8 + - - +
28A THR* 3.6 5.3 + - - +
29A VAL* 3.4 33.3 - - + +
30A GLU* 2.9 44.3 + - - +
65A TYR* 4.0 13.8 + - + +
87A ILE* 3.9 19.7 - - + -
313A SER* 3.2 30.0 + - - +
314A ILE* 3.3 5.0 + - - +
316A MET* 1.3 74.2 - - + +
318A GLU* 1.3 61.0 + - - +
320A ALA* 3.8 2.6 - - - +
321A ALA* 3.0 28.9 + - - +
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Residues in contact with GLU 318 (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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29A VAL* 3.8 16.2 - - + +
33A ILE* 3.8 22.1 - - + +
314A ILE* 3.0 39.3 + - - +
315A GLU* 3.9 5.8 - - - +
317A ARG* 1.3 75.0 - - - +
319A GLU* 1.3 59.8 + - - +
321A ALA* 3.4 2.8 + - - +
322A ARG* 2.9 52.9 + - - +
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Residues in contact with GLU 319 (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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109A VAL* 4.2 22.9 - - + -
315A GLU* 3.2 18.1 + - + +
316A MET 3.9 3.1 - - - +
318A GLU* 1.3 74.7 - - - +
320A ALA* 1.3 59.0 - - - +
322A ARG* 3.1 25.8 + - - +
323A GLU* 2.9 29.1 + - + +
326A ARG* 3.1 28.8 + - - -
337A LYS* 3.4 28.8 + - - +
338A ASN* 4.0 12.9 + - - +
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Residues in contact with ALA 320 (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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30A GLU* 5.9 0.2 - - + -
63A LEU* 3.9 7.0 - - + -
85A VAL* 3.8 22.4 - - + +
87A ILE* 3.7 28.3 - - + -
109A VAL* 3.9 8.4 - - + +
316A MET 2.9 20.2 + - - +
317A ARG 3.8 4.9 - - - +
319A GLU* 1.3 74.3 - - - +
321A ALA* 1.3 63.3 + - - +
323A GLU* 3.1 6.1 + - - +
324A ILE* 3.1 25.1 + - - +
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Residues in contact with ALA 321 (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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30A GLU* 3.9 25.3 - - + +
33A ILE* 3.8 26.2 - - + +
34A LEU* 3.2 20.3 - - + +
63A LEU* 4.7 1.5 - - - +
317A ARG 3.0 19.0 + - - +
318A GLU 3.6 4.9 - - - +
320A ALA* 1.3 75.6 - - - +
322A ARG* 1.3 63.6 + - - +
324A ILE* 3.4 5.1 + - - -
325A ARG* 3.2 18.4 + - - +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.1 20.2 - - + +
315A GLU* 4.7 2.8 + - - +
318A GLU* 2.9 49.8 + - - +
319A GLU* 3.1 28.6 + - - +
321A ALA* 1.3 73.2 - - - +
323A GLU* 1.3 59.6 + - - +
325A ARG* 3.4 6.6 + - + +
326A ARG* 3.0 54.8 + - - +
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Residues in contact with GLU 323 (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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85A VAL* 3.8 14.7 - - + +
107A CYS* 3.3 37.6 - - + +
108A ASN 4.8 1.6 - - - +
319A GLU* 2.9 13.4 + - + +
320A ALA* 3.1 9.6 + - - +
322A ARG* 1.3 75.8 - - - +
324A ILE* 1.3 64.5 + - - +
326A ARG* 2.7 31.9 + - - +
327A ALA* 3.1 21.7 + - - +
336A LEU* 3.5 12.5 - - + +
337A LYS 2.9 17.1 + - - -
338A ASN* 2.8 33.9 + - - +
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Residues in contact with ILE 324 (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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19A VAL* 3.8 39.0 - - + -
34A LEU* 3.8 17.0 - - + -
61A GLY* 4.5 0.7 - - - -
62A ALA 3.9 21.5 - - - +
63A LEU* 3.7 20.2 - - + -
83A ILE* 4.4 13.7 - - + -
85A VAL* 3.8 18.8 - - + -
320A ALA 3.1 14.5 + - - +
321A ALA* 3.5 8.3 - - - +
322A ARG 3.3 0.2 - - - -
323A GLU* 1.3 76.7 - - - +
325A ARG* 1.3 62.3 + - - +
327A ALA* 3.1 16.4 + - - +
328A ILE* 3.1 21.2 + - + +
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Residues in contact with ARG 325 (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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32A PRO 5.1 1.4 + - - -
33A ILE* 2.7 40.5 + - + +
34A LEU* 4.2 7.6 - - + -
36A ASP* 2.7 43.4 + - - -
37A VAL* 3.7 29.8 - - + +
321A ALA 3.2 10.4 + - - +
322A ARG* 3.7 12.3 - - + +
323A GLU 3.3 0.2 - - - -
324A ILE* 1.3 79.9 - - - +
326A ARG* 1.3 51.3 + - - +
328A ILE* 3.3 3.2 + - - +
329A THR* 2.8 49.9 + - + +
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Residues in contact with ARG 326 (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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319A GLU* 3.1 25.9 + - - -
322A ARG* 3.0 42.8 + - + +
323A GLU* 2.7 48.9 + - - +
325A ARG* 1.3 75.3 - - + +
327A ALA* 1.3 57.5 + - - +
329A THR* 4.0 5.2 - - - -
330A GLY* 3.0 22.1 + - - +
335A SER* 3.3 46.2 - - - +
336A LEU* 4.7 1.3 - - + +
337A LYS* 3.5 25.9 - - - +
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Residues in contact with ALA 327 (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 ILE* 3.9 25.6 - - + -
323A GLU 3.1 11.8 + - - +
324A ILE 3.1 10.7 + - - +
326A ARG* 1.3 77.4 - - - +
328A ILE* 1.3 62.1 + - + +
330A GLY 3.6 13.0 - - - +
332A ILE* 3.5 35.8 - - + +
336A LEU* 4.0 8.7 - - + +
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Residues in contact with ILE 328 (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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17A PRO* 3.8 30.3 - - + -
19A VAL* 4.0 8.5 - - + -
37A VAL* 4.0 22.0 - - + +
38A ALA* 3.8 29.4 - - + -
60A VAL* 5.6 7.9 - - + -
61A GLY* 6.3 0.7 - - - +
83A ILE* 5.8 2.9 - - + -
324A ILE* 3.1 31.6 + - + +
325A ARG* 4.0 3.6 - - - +
327A ALA* 1.3 80.0 - - + +
329A THR* 1.3 64.7 + - + +
330A GLY 4.4 1.9 - - - +
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Residues in contact with THR 329 (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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37A VAL* 4.2 26.5 - - + -
325A ARG* 2.8 34.6 + - + +
326A ARG* 4.0 4.0 - - - -
328A ILE* 1.3 81.0 - - + +
330A GLY* 1.3 62.4 + - - +
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Residues in contact with GLY 330 (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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326A ARG 3.0 11.8 + - - -
327A ALA 3.6 9.9 - - - +
328A ILE 4.4 1.4 - - - +
329A THR* 1.3 87.0 + - - +
331A ARG* 1.3 67.2 + - - +
332A ILE* 4.3 0.3 + - - +
335A SER* 3.3 13.5 - - - -
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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
------------------------------------------------------------
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