Contacts of the helix formed by residues 287 - 307 (chain A) in PDB entry 3W5D
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 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLY* 1.3 74.7 - - - -
288A TRP* 1.3 62.4 + - - +
289A ILE* 4.7 5.6 - - - -
290A ARG* 3.4 49.6 + - - +
291A GLY* 3.0 20.4 + - - -
875A GLN* 3.8 7.3 + - - -
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Residues in contact with TRP 288 (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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282A PRO 5.5 1.8 + - - -
283A VAL* 4.2 40.5 + - + -
285A GLY 5.0 4.7 + - - -
286A GLY* 3.9 9.5 + - - -
287A SER* 1.3 73.0 - - - +
289A ILE* 1.3 68.6 + - - +
290A ARG 3.2 0.2 - - - -
291A GLY* 3.0 3.5 + - - +
292A ALA* 2.9 23.7 + - - +
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.0 33.4 - - + +
287A SER* 4.7 6.5 - - - -
288A TRP* 1.3 79.1 - - - +
290A ARG* 1.3 70.9 + - + +
292A ALA* 3.4 6.3 + - + +
293A ILE* 3.0 49.6 + - + +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER* 3.4 29.5 + - - +
288A TRP 3.2 0.6 - - - -
289A ILE* 1.3 82.6 - - + +
291A GLY* 1.3 60.9 + - - +
293A ILE* 3.4 13.6 + - + +
294A TYR* 3.0 27.2 + - - +
874A MET 4.4 10.1 + - - -
875A GLN* 3.5 51.3 + - - +
877A THR* 4.3 4.6 + - - -
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER 3.0 13.0 + - - -
288A TRP* 3.0 9.4 + - - -
290A ARG* 1.3 78.0 - - - +
292A ALA* 1.3 55.8 + - - +
294A TYR* 3.3 11.6 - - - +
295A TYR* 3.2 30.6 - - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TRP 2.9 14.6 + - - +
289A ILE* 3.9 7.6 - - + +
291A GLY* 1.3 72.3 - - - +
293A ILE* 1.3 66.5 + - - +
294A TYR 3.0 2.0 - - - -
295A TYR* 3.1 6.3 + - - +
296A PHE* 2.9 48.7 + - + -
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 22.4 - - + +
78A PHE* 4.3 18.8 - - + +
79A GLU* 6.0 2.9 - - + -
289A ILE* 3.0 44.6 + - + +
290A ARG* 3.7 15.5 - - + +
291A GLY 3.4 0.2 - - - -
292A ALA* 1.3 76.7 - - + +
294A TYR* 1.3 57.1 + - - +
296A PHE* 4.8 4.0 - - - +
297A LYS* 3.0 47.1 + - + +
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Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 5.7 4.5 - - + -
275A ASN* 4.3 13.9 - - - -
290A ARG 3.0 14.3 + - - +
291A GLY* 3.3 13.2 - - - +
292A ALA 3.0 0.2 - - - -
293A ILE* 1.3 78.6 - - - +
295A TYR* 1.3 80.1 + + - +
297A LYS* 3.8 5.9 - - + +
298A ILE* 3.4 37.7 + - + +
778A THR 4.5 2.4 + - - -
779A ALA* 3.6 35.4 + - + -
782A GLY* 4.5 7.8 - - - -
783A LEU 4.8 7.6 + - - -
785A GLU* 5.9 8.7 - - + -
874A MET* 5.6 9.8 - - + -
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Residues in contact with TYR 295 (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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271A VAL* 4.8 12.6 - - + -
272A TRP* 4.3 32.2 - + + -
275A ASN* 2.9 43.8 + - + +
278A HIS* 4.2 13.0 - + - +
291A GLY* 3.2 19.1 - - - -
292A ALA* 3.1 8.7 + - - +
294A TYR* 1.3 89.8 - + - +
296A PHE* 1.3 67.4 + - + +
298A ILE* 3.1 12.3 - - + +
299A ALA* 2.8 29.9 + - - +
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Residues in contact with PHE 296 (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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71A ILE* 3.5 39.3 - - + -
75A LEU* 4.1 17.3 - - + -
292A ALA* 2.9 44.0 + - + +
293A ILE* 4.4 0.9 - - - +
295A TYR* 1.3 79.3 - - + +
297A LYS* 1.3 61.3 + - - +
299A ALA* 3.9 9.3 - - + +
300A VAL* 3.2 31.2 + - - +
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Residues in contact with LYS 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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75A LEU* 3.9 19.1 - - + +
79A GLU* 4.9 11.9 + - - -
293A ILE* 3.0 35.9 + - + +
294A TYR* 3.8 8.3 - - + +
295A TYR 3.2 0.2 - - - -
296A PHE* 1.3 78.4 - - - +
298A ILE* 1.3 59.6 + - - +
300A VAL* 3.8 4.9 + - - +
301A ALA* 3.3 21.1 + - - +
785A GLU* 4.0 32.6 - - - +
789A PRO* 5.2 2.1 - - - +
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Residues in contact with ILE 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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268A CYS* 6.1 1.6 - - - -
271A VAL* 3.3 47.1 - - + -
294A TYR* 3.4 29.4 + - + +
295A TYR* 3.1 21.1 + - + +
297A LYS* 1.3 73.9 - - - +
299A ALA* 1.3 57.8 + - + +
300A VAL 3.2 2.0 - - - -
301A ALA* 3.9 5.1 - - - +
302A LEU* 2.7 47.2 + - + +
775A ILE* 4.4 12.4 - - + +
778A THR* 5.9 3.1 - - + -
779A ALA* 4.4 18.8 - - + -
785A GLU* 4.2 16.4 - - + +
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Residues in contact with ALA 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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68A ALA* 5.4 0.2 - - - +
71A ILE* 6.1 0.7 - - + -
268A CYS* 4.3 20.8 - - - -
295A TYR 2.8 17.8 + - - +
296A PHE* 3.9 14.4 - - + +
298A ILE* 1.3 78.1 - - + +
300A VAL* 1.3 60.2 + - + +
302A LEU* 3.5 7.6 - - - +
303A ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 3.6 38.3 - - + +
71A ILE* 3.7 20.6 - - + -
72A SER* 4.1 6.7 - - - +
75A LEU* 5.5 2.2 - - + -
90A GLU* 3.7 23.3 - - - +
94A ILE* 4.6 2.7 - - + -
296A PHE 3.2 18.4 + - - +
297A LYS* 3.9 5.6 - - - +
298A ILE 3.2 0.2 - - - -
299A ALA* 1.3 76.0 - - + +
301A ALA* 1.3 65.4 + - - +
302A LEU 3.3 0.2 + - - -
303A ALA* 3.3 4.0 + - - +
304A VAL* 2.9 31.9 + - + +
789A PRO* 4.1 9.6 - - + -
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Residues in contact with ALA 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 LYS 3.3 14.2 + - - +
298A ILE* 3.3 7.0 + - - +
300A VAL* 1.3 78.8 - - - +
302A LEU* 1.3 52.6 + - - +
304A VAL* 3.6 2.6 - - - -
305A ALA* 2.7 39.8 + - - +
775A ILE* 4.2 22.7 - - + -
785A GLU* 5.6 2.9 - - - +
787A LEU 5.0 2.7 - - - +
789A PRO* 3.8 27.6 - - + -
792A LEU* 3.7 5.1 - - + +
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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
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264A ILE* 3.7 38.6 - - + +
267A ILE* 3.5 38.4 - - + +
268A CYS* 3.8 16.4 - - - +
271A VAL* 4.6 2.7 - - + -
298A ILE* 2.7 40.4 + - + +
299A ALA 3.5 4.0 - - - +
301A ALA* 1.3 73.5 - - - +
303A ALA* 1.3 61.8 + - - +
305A ALA* 3.4 5.5 + - - +
306A ALA* 3.1 25.7 + - + +
772A VAL* 4.4 8.8 - - + +
775A ILE* 4.5 16.8 - - + +
776A PHE* 5.5 2.2 - - + +
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Residues in contact with ALA 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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64A ILE* 3.6 28.5 - - + -
65A LEU* 4.9 2.5 - - + -
68A ALA* 4.4 13.7 - - + -
264A ILE* 4.1 16.8 - - + -
299A ALA 3.0 17.2 + - - +
300A VAL 3.7 4.3 - - - +
302A LEU* 1.3 76.8 - - - +
304A VAL* 1.3 62.8 + - + +
306A ALA* 3.3 2.3 + - - +
307A ILE* 3.2 30.5 + - - +
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Residues in contact with VAL 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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65A LEU* 4.6 13.7 - - + -
68A ALA* 5.0 3.4 - - + -
94A ILE* 4.2 25.1 - - + -
300A VAL* 2.9 23.5 + - + +
301A ALA* 3.7 6.5 - - - +
303A ALA* 1.3 75.9 - - - +
305A ALA* 1.3 62.5 + - - +
307A ILE 3.7 0.5 - - - +
309A GLU* 2.5 29.7 - - - +
789A PRO* 3.8 19.5 - - + +
792A LEU* 3.9 13.9 - - + -
793A LEU* 3.8 31.2 - - + -
796A ASN* 3.7 3.6 + - - -
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Residues in contact with ALA 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 ALA 2.7 22.2 + - - +
302A LEU 3.9 4.3 - - - +
303A ALA 3.3 0.2 - - - -
304A VAL* 1.3 72.4 - - - +
306A ALA* 1.3 57.3 + - - +
768A ASN* 3.2 30.8 + - - +
771A GLU* 3.3 40.7 - - + +
772A VAL* 4.0 4.9 - - + +
775A ILE* 4.1 6.5 - - + -
792A LEU* 3.7 15.3 - - + -
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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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256A PHE* 5.3 1.4 - - - -
260A LEU* 3.5 25.2 - - + +
263A VAL* 6.4 0.4 - - + -
264A ILE* 3.7 29.4 - - + -
267A ILE* 6.3 1.8 - - + -
302A LEU* 3.1 17.4 + - + +
303A ALA 3.8 0.2 - - - +
304A VAL 3.2 0.6 - - - -
305A ALA* 1.3 79.3 - - - +
307A ILE* 1.3 63.5 + - - +
308A PRO* 3.6 3.1 - - - +
768A ASN* 3.7 12.1 - - - +
772A VAL* 3.8 16.6 - - + -
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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
----------------------------------------------------------
61A LEU* 3.6 45.5 - - + +
64A ILE* 4.9 4.5 - - + -
65A LEU* 3.9 27.8 - - + -
260A LEU* 3.8 6.3 - - + -
264A ILE* 3.8 21.5 - - + -
303A ALA 3.2 15.1 + - - +
304A VAL 3.7 0.4 + - - +
305A ALA 3.6 0.2 - - - -
306A ALA* 1.3 76.5 - - - +
308A PRO* 1.3 71.2 - - + +
309A GLU* 2.8 51.0 + - + +
768A ASN* 3.2 10.9 + - - -
796A ASN* 3.7 0.7 + - - -
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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