Contacts of the helix formed by residues 298 - 319 (chain D) in PDB entry 2WWR
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 THR 298 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ARG* 3.6 26.2 - - - +
147C CYS* 4.3 4.7 - - - -
148C GLY 3.2 15.7 - - - +
150C GLY* 3.8 19.7 - - - +
110D THR* 3.7 15.1 + - + +
296D SER 3.0 7.7 + - - -
297D ALA* 1.3 78.4 - - - +
299D HIS* 1.3 65.8 + - - +
300D ARG* 4.0 5.2 + - - +
301D THR* 3.2 28.2 + - - -
302D ARG* 2.9 26.0 + - - +
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Residues in contact with HIS 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 6.0 0.2 - - - -
144C LEU* 6.0 3.8 - - + +
147C CYS* 3.4 30.9 + - + +
148C GLY 3.3 15.3 + - - +
149C TYR* 3.5 45.3 + + + -
298D THR* 1.3 72.1 - - - +
300D ARG* 1.3 65.7 + - + +
302D ARG* 4.1 2.7 - - - +
303D ASN* 3.1 37.2 + - - +
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Residues in contact with ARG 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 5.1 9.1 + - - -
153C GLN* 4.3 23.9 + - - +
298D THR* 3.4 5.6 + - - +
299D HIS* 1.3 78.8 - - + +
301D THR* 1.3 52.5 + - - +
303D ASN* 3.5 7.0 + - - +
304D THR* 2.6 42.9 + - - +
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Residues in contact with THR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D VAL 4.0 11.9 + - - +
107D LEU* 4.0 14.1 - - + -
110D THR* 2.6 25.4 + - - +
296D SER* 3.4 28.3 - - - +
298D THR* 3.2 16.2 + - - -
300D ARG* 1.3 76.1 - - - +
302D ARG* 1.3 60.4 + - - +
304D THR* 3.1 7.0 + - - -
305D MET* 2.8 49.3 + - + +
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TRP* 3.3 38.2 - - - +
142C LYS 3.3 24.5 + - - -
143C PRO* 3.3 27.0 - - - +
144C LEU* 5.6 1.8 - - + -
145C TRP 4.6 4.6 + - - -
147C CYS* 3.9 13.4 - - - -
16D PRO* 3.4 11.7 - - + +
81D MET* 3.6 7.5 - - - +
293D HIS 4.4 7.1 + - - -
296D SER* 2.8 40.3 + - - +
297D ALA* 3.3 27.0 - - - +
298D THR 2.9 23.0 + - - +
299D HIS* 4.2 2.5 - - - +
301D THR* 1.3 72.8 - - - +
303D ASN* 1.3 57.8 + - - +
305D MET* 3.6 7.9 + - - -
306D SER* 3.0 27.7 + - - -
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Residues in contact with ASN 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 5.7 0.5 - - - +
16D PRO* 3.3 22.6 - - - +
17D ALA* 3.9 10.2 + - - +
18D GLU* 4.0 34.6 + - - +
299D HIS* 3.1 32.0 + - - +
300D ARG* 3.6 6.5 - - - +
302D ARG* 1.3 74.5 - - - +
304D THR* 1.3 59.7 + - - +
306D SER* 3.1 5.1 + - - -
307D LEU* 2.9 28.8 + - - +
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Residues in contact with THR 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLU* 4.9 3.9 + - - +
106D VAL* 3.4 30.3 - - + -
300D ARG* 2.6 31.7 + - - +
301D THR* 3.7 5.1 - - - -
303D ASN* 1.3 72.7 - - - +
305D MET* 1.3 56.7 + - - +
307D LEU* 3.3 13.6 + - + +
308D LEU* 2.8 41.0 + - + +
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Residues in contact with MET 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TRP* 4.4 12.1 - - + -
81D MET* 3.6 35.0 - - + +
82D SER* 4.3 3.6 - - - -
103D THR* 3.5 21.0 - - + +
106D VAL* 4.0 19.0 - - + +
107D LEU* 3.9 19.7 - - + -
296D SER* 3.5 26.0 - - - +
301D THR* 2.8 31.0 + - + +
302D ARG* 3.7 14.8 - - - +
304D THR* 1.3 76.1 - - - +
306D SER* 1.3 52.2 + - - +
308D LEU* 3.2 1.2 + - - -
309D ALA* 2.8 37.4 + - - +
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Residues in contact with SER 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 3.6 10.1 - - - +
16D PRO* 2.8 44.9 + - - +
19D GLY* 3.2 12.6 + - - -
56D LEU* 5.1 0.3 - - - +
81D MET* 3.9 12.5 - - - +
302D ARG 3.0 15.6 + - - -
303D ASN 3.1 9.9 - - - -
305D MET* 1.3 76.6 - - - +
307D LEU* 1.3 56.4 + - - +
309D ALA* 3.5 2.6 + - - +
310D ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLU* 3.7 40.8 - - + +
19D GLY* 3.9 7.4 - - - -
22D ALA* 4.1 12.8 - - + -
303D ASN 2.9 15.7 + - - +
304D THR* 3.8 13.0 - - + +
306D SER* 1.3 74.0 - - - +
308D LEU* 1.3 61.6 + - - +
310D ALA* 3.2 2.0 + - - +
311D ASN* 2.9 49.8 + - - +
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D THR* 3.7 25.6 - - + -
104D PRO 4.4 4.0 - - - +
106D VAL* 4.0 29.2 - - + -
304D THR* 2.8 23.6 + - + +
305D MET 3.7 2.9 - - - +
307D LEU* 1.3 74.1 - - - +
309D ALA* 1.3 57.4 + - - +
311D ASN* 3.6 5.5 + - + +
312D ASN* 2.8 41.3 + - - +
323D PRO* 4.0 29.1 - - + +
324D SER* 4.2 13.5 - - - +
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Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 4.0 14.8 - - + +
79D SER* 2.7 33.3 + - - +
80D THR 4.2 3.1 - - - +
81D MET* 4.1 29.2 - - + -
103D THR* 3.9 3.5 - - + +
305D MET 2.8 17.9 + - - +
306D SER 3.6 4.9 - - - +
308D LEU* 1.3 75.4 - - - +
310D ALA* 1.3 63.3 + - - +
312D ASN* 4.3 3.1 - - - +
313D LEU* 3.2 11.6 + - - +
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Residues in contact with ALA 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLY* 3.6 26.9 - - - +
22D ALA* 4.0 13.2 - - + -
23D LEU* 4.1 11.1 - - + +
56D LEU* 4.1 11.0 - - + -
306D SER 2.9 17.0 + - - +
307D LEU 3.2 5.6 + - - +
309D ALA* 1.3 76.1 - - - +
311D ASN* 1.3 57.9 + - - +
313D LEU* 3.3 4.3 + - - +
314D LEU* 3.1 32.9 + - - +
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Residues in contact with ASN 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA* 4.6 7.3 - - - +
307D LEU* 2.9 42.3 + - - +
308D LEU* 4.1 7.5 - - + +
310D ALA* 1.3 75.9 - - - +
312D ASN* 1.3 58.4 + - - +
314D LEU* 3.9 14.2 - - - +
315D ALA* 2.9 32.4 + - - +
323D PRO* 4.5 17.7 - - + +
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Residues in contact with ASN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 4.2 1.9 - - - +
79D SER* 3.6 14.1 - - - +
101D GLY* 4.3 2.4 - - - -
102D TYR 3.5 20.2 + - - +
308D LEU* 2.8 30.3 + - - +
309D ALA* 4.3 2.6 - - - +
311D ASN* 1.3 77.0 - - - +
313D LEU* 1.3 63.2 + - - +
316D GLY* 3.1 18.5 + - - -
322D MET* 3.3 35.5 - - + +
323D PRO* 3.3 4.0 - - - +
324D SER* 3.0 43.9 + - - +
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.8 23.8 - - + -
23D LEU* 3.7 25.4 - - + -
54D GLY* 3.8 11.2 - - - -
55D LEU 3.5 37.9 - - - +
56D LEU* 4.1 18.4 - - + +
77D VAL* 3.5 22.6 - - + +
79D SER* 3.8 11.6 - - - -
309D ALA 3.2 11.7 + - - +
310D ALA 3.5 7.4 - - - +
312D ASN* 1.3 78.4 - - - +
314D LEU* 1.3 56.2 + - - +
316D GLY 3.3 1.6 + - - -
317D LEU* 3.0 32.7 + - + +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA* 4.2 23.1 - - + +
23D LEU* 4.1 19.1 - - + -
26D ALA* 3.8 24.5 - - + -
29D CYS* 3.8 21.8 - - - -
310D ALA 3.1 23.7 + - - +
311D ASN* 3.9 15.0 - - - +
313D LEU* 1.3 72.7 - - - +
315D ALA* 1.3 66.9 + - - +
317D LEU* 3.2 6.7 + - + -
318D ARG* 3.1 55.5 + - - +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D ASN 2.9 19.0 + - - +
313D LEU 3.4 0.2 - - - -
314D LEU* 1.3 75.1 - - - +
316D GLY* 1.3 57.3 + - - +
318D ARG* 4.9 2.5 - - - +
319D GLY 3.0 6.9 + - - -
320D GLU* 2.9 45.5 + - + +
321D PRO 3.4 24.5 - - - +
322D MET* 3.7 15.9 - - + -
323D PRO* 4.8 2.2 - - + -
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Residues in contact with GLY 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LYS* 4.6 10.7 + - - +
77D VAL* 3.9 20.4 - - - -
99D ARG* 3.8 22.7 + - - -
312D ASN 3.1 13.2 + - - -
313D LEU 3.8 3.1 - - - -
314D LEU 3.2 0.2 - - - -
315D ALA* 1.3 74.1 - - - +
317D LEU* 1.3 60.4 + - - +
318D ARG 3.1 6.1 + - - -
319D GLY* 3.5 9.5 + - - -
322D MET* 4.4 2.8 - - - +
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Residues in contact with LEU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D MET* 3.3 40.3 - - + +
9D VAL* 3.4 28.5 - - + -
29D CYS* 3.6 18.2 - - - -
53D HIS* 3.3 46.4 - - + +
54D GLY 3.8 1.6 - - - +
76D LYS* 3.4 18.5 + - + -
77D VAL* 3.6 8.8 - - + +
313D LEU* 3.0 29.8 + - + +
314D LEU* 3.2 7.4 + - + +
316D GLY* 1.3 74.3 - - - +
318D ARG* 1.3 59.1 + - + +
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Residues in contact with ARG 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D MET* 4.9 1.3 - - + -
26D ALA* 3.7 21.6 - - - +
28D ASP* 2.6 47.9 + - - +
29D CYS* 5.6 0.6 - - - -
76D LYS* 5.5 1.6 + - - -
314D LEU* 3.1 44.2 + - - +
315D ALA 4.1 2.7 - - - +
316D GLY 3.1 0.6 - - - -
317D LEU* 1.3 83.6 - - + +
319D GLY* 1.3 57.2 - - - +
320D GLU* 3.8 24.7 + - + +
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Residues in contact with GLY 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG* 4.0 8.1 + - - -
315D ALA 3.0 4.5 + - - -
316D GLY 3.5 8.3 + - - -
318D ARG* 1.3 78.9 - - - +
320D GLU* 1.3 68.0 + - - +
321D PRO* 4.7 0.9 - - - +
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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
------------------------------------------------------------
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