Contacts of the helix formed by residues 281 - 298 (chain A) in PDB entry 1W7L
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 PRO 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A VAL* 5.3 7.9 - - + -
254A TRP 6.1 0.9 - - - +
255A LYS 5.8 4.5 - - - +
256A VAL* 6.1 1.8 - - + -
279A HIS 4.7 0.7 - - - +
280A CYS* 1.3 89.0 - - + +
282A THR* 1.3 64.1 + - - +
283A GLN 4.9 1.6 - - - +
284A SER* 3.7 20.0 + - - +
285A GLN* 3.1 23.4 + - + +
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Residues in contact with THR 282 (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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59A MET 5.1 0.2 - - - +
60A LEU* 3.2 47.6 - - + +
61A ASN 5.4 0.4 - - - -
62A GLN 2.7 22.2 + - - +
63A TYR* 3.7 1.4 - - - -
64A THR* 3.2 36.7 + - - +
69A TYR* 4.2 6.5 - - + -
280A CYS 3.5 1.1 + - - -
281A PRO* 1.3 72.8 - - - +
283A GLN* 1.3 62.3 + - - +
285A GLN* 3.2 7.1 + - - +
286A ALA* 3.1 23.7 + - - +
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Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.9 13.5 - - + -
53A ALA* 3.4 42.6 + - + +
54A VAL* 3.8 21.1 + - + +
60A LEU* 3.2 28.8 + - + +
61A ASN* 2.9 39.3 + - - +
281A PRO* 3.6 1.4 - - - +
282A THR* 1.3 75.4 - - - +
284A SER* 1.3 61.0 + - - +
286A ALA* 3.1 4.8 + - - -
287A ALA* 2.9 25.1 + - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.6 28.8 - - - -
254A TRP* 4.3 13.7 + - - -
256A VAL* 3.4 24.8 - - - +
281A PRO* 3.7 25.4 + - - +
283A GLN* 1.3 78.1 - - - +
285A GLN* 1.3 58.2 + - - +
287A ALA* 3.2 6.2 + - - +
288A VAL* 2.9 32.1 + - - +
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Residues in contact with GLN 285 (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 THR* 3.5 17.0 - - - +
65A LYS 5.1 0.6 + - - -
68A GLY* 3.4 5.4 - - - -
69A TYR* 2.7 38.4 + - + +
72A LEU* 3.7 19.2 - - + +
96A VAL* 3.4 30.0 - - + +
256A VAL* 4.6 6.5 - - + -
280A CYS* 3.3 26.7 + - + +
281A PRO* 3.1 22.4 + - + +
282A THR 3.2 9.9 + - - +
284A SER* 1.3 81.9 + - - +
286A ALA* 1.3 57.2 + - - +
288A VAL* 3.2 4.5 + - - +
289A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 286 (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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49A ALA 5.0 0.7 - - - -
53A ALA* 3.9 14.8 - - + -
60A LEU* 4.8 9.9 - - + -
69A TYR* 3.5 33.3 - - + +
282A THR 3.1 11.7 + - - +
283A GLN* 3.1 10.7 + - - +
285A GLN* 1.3 74.6 - - - +
287A ALA* 1.3 63.6 + - - +
289A ALA* 3.4 2.8 + - - +
290A GLU* 3.1 24.6 + - - +
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Residues in contact with ALA 287 (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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49A ALA* 3.4 15.0 - - - +
50A PHE* 3.5 38.6 - - + +
53A ALA* 4.3 0.6 - - - +
254A TRP* 3.8 15.9 - - + -
283A GLN 2.9 11.3 + - - +
284A SER* 3.2 9.4 + - - +
286A ALA* 1.3 77.0 - - - +
288A VAL* 1.3 52.3 + - - +
290A GLU 3.5 0.3 + - - -
291A SER* 2.8 36.8 + - - -
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Residues in contact with VAL 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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72A LEU* 3.7 22.4 - - + -
245A ALA* 3.5 31.0 - - + -
249A PHE* 4.4 3.1 - - + -
254A TRP* 3.6 19.3 - - + -
256A VAL* 4.0 13.5 - - + -
258A TRP* 4.4 4.5 - - + -
284A SER 2.9 21.0 + - - +
285A GLN 3.7 5.4 - - - +
287A ALA* 1.3 73.0 - - - +
289A ALA* 1.3 59.8 + - - +
291A SER* 3.3 6.6 + - - -
292A PHE* 2.9 49.3 + - + -
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Residues in contact with ALA 289 (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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69A TYR* 4.7 0.7 - - + -
71A PRO* 3.8 13.0 - - + +
72A LEU* 3.7 36.0 - - - +
75A ILE* 3.9 5.7 - - + +
285A GLN 2.9 16.8 + - - +
286A ALA* 3.6 9.0 - - - +
288A VAL* 1.3 76.5 - - - +
290A GLU* 1.3 56.9 + - - +
292A PHE* 3.3 3.8 + - - +
293A GLU* 3.0 39.0 + - - +
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Residues in contact with GLU 290 (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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45A PHE 4.6 2.2 - - - +
48A GLU* 5.4 0.2 - - - +
49A ALA* 3.3 24.5 + - + +
52A HIS* 2.9 40.0 + - - +
286A ALA 3.1 16.1 + - - +
287A ALA* 3.8 3.8 - - - +
289A ALA* 1.3 76.0 - - - +
291A SER* 1.3 61.7 + - - +
293A GLU* 3.5 16.2 + - + +
294A ARG* 3.1 22.2 + - + +
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Residues in contact with SER 291 (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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45A PHE* 3.5 21.3 - - - -
46A ALA* 3.6 23.4 + - - +
49A ALA* 3.7 3.5 - - - +
249A PHE* 3.6 35.1 - - - -
254A TRP* 4.3 2.6 - - - -
287A ALA 2.8 22.9 + - - -
288A VAL* 3.3 4.2 + - - -
290A GLU* 1.3 77.7 - - - +
292A PHE* 1.3 56.4 + - - +
294A ARG* 3.5 4.2 + - - +
295A GLU* 3.1 21.3 + - - +
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Residues in contact with PHE 292 (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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72A LEU* 4.6 2.5 - - + -
75A ILE* 3.8 19.3 - - + -
76A LEU* 3.9 15.5 - - + -
79A PHE* 3.8 33.3 - + + -
80A PHE* 3.9 16.4 - + - -
218A TRP* 4.8 0.7 - - - -
248A THR* 3.9 13.7 - - + -
249A PHE* 3.9 16.2 - + - -
258A TRP* 3.5 36.6 - + - -
288A VAL* 2.9 40.9 + - + +
289A ALA 3.8 3.8 - - - +
291A SER* 1.3 73.6 - - - +
293A GLU* 1.3 56.3 + - - +
295A GLU* 3.2 1.7 + - - +
296A GLN* 2.7 36.9 + - - +
306A PHE* 4.0 13.5 - + - -
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Residues in contact with GLU 293 (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 PRO* 4.4 17.2 - - - +
75A ILE* 4.0 23.2 - - + +
289A ALA* 3.0 29.5 + - - +
290A GLU* 3.7 14.4 - - - +
292A PHE* 1.3 75.1 - - - +
294A ARG* 1.3 57.9 + - - +
296A GLN* 3.9 3.2 - - - +
297A LEU* 3.0 30.0 + - - +
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Residues in contact with ARG 294 (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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45A PHE* 3.4 53.9 - - + +
290A GLU* 3.1 14.5 + - + +
291A SER 3.5 8.7 - - - +
293A GLU* 1.3 77.4 - - - +
295A GLU* 1.3 90.6 + - - +
297A LEU* 3.4 9.8 + - + +
298A LEU* 3.2 44.2 + - + +
303A SER* 3.6 15.6 + - - -
305A TYR* 3.6 11.9 - - - +
308A GLN* 5.4 1.6 + - - -
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Residues in contact with GLU 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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45A PHE* 3.8 10.5 - - + -
79A PHE* 4.9 2.0 - - + -
249A PHE* 4.0 1.3 - - + -
291A SER 3.1 15.2 + - - +
292A PHE* 3.2 5.4 + - + +
294A ARG* 1.3 108.8 + - - +
296A GLN* 1.3 60.6 + - - +
298A LEU* 3.5 1.7 - - - +
299A PHE* 3.0 32.1 + - - +
304A SER* 3.4 11.3 - - - -
305A TYR* 2.9 19.2 + - - +
306A PHE* 2.9 63.7 + - + +
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Residues in contact with GLN 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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75A ILE* 3.3 23.6 - - + +
78A SER* 2.8 29.4 + - - -
79A PHE* 3.6 39.0 - - + +
82A GLU* 6.0 1.0 - - - +
292A PHE 2.7 22.2 + - - +
293A GLU* 3.9 4.4 - - - +
295A GLU* 1.3 71.7 - - - +
297A LEU* 1.3 64.8 + - - +
299A PHE* 3.4 14.6 + - + +
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Residues in contact with LEU 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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293A GLU 3.0 17.9 + - - +
294A ARG* 3.5 9.9 - - + +
296A GLN* 1.3 79.1 + - - +
298A LEU* 1.3 71.3 + - + +
299A PHE 3.6 1.2 + - - -
301A GLN* 3.4 14.0 + - - -
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Residues in contact with LEU 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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294A ARG* 3.2 56.6 + - + +
295A GLU* 3.5 3.8 - - - +
296A GLN 3.3 0.2 - - - -
297A LEU* 1.3 93.0 - - + +
299A PHE* 1.3 64.3 + - - +
301A GLN* 2.9 42.2 + - + +
303A SER* 3.7 20.6 - - - +
304A SER* 3.2 20.5 - - - -
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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
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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