Contacts of the helix formed by residues 291 - 305 (chain A) in PDB entry 4WLP
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 TYR 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ARG* 2.5 30.0 + - - +
287A ARG 4.9 1.6 - - - -
289A HIS* 3.2 52.3 + + + +
290A ASN* 1.3 74.1 + - - +
292A LEU* 1.3 66.2 + - - +
293A PRO 3.4 2.0 - - - -
294A PHE* 3.3 17.3 + + + +
295A ILE* 2.9 32.5 + - + +
74B LEU* 4.0 27.1 - - + -
75B PRO* 4.1 7.7 - - + +
88B LEU* 5.4 2.7 - - + +
92B LEU* 4.6 12.6 - - + -
98B PHE* 3.0 30.9 - + - -
103B PRO* 3.8 28.9 - - + -
104B LEU* 5.8 0.7 - - + -
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Residues in contact with LEU 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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290A ASN* 3.5 17.3 - - - +
291A TYR* 1.3 74.7 - - - +
293A PRO* 1.3 75.6 - - + +
295A ILE* 2.9 9.9 + - + +
296A MET* 2.8 39.8 + - + +
103B PRO 5.5 0.7 - - - +
107B ALA* 3.6 33.7 - - + -
110B LEU* 4.8 8.1 - - + -
111B PHE* 5.3 1.1 - - + -
116B PHE* 3.7 34.3 - - + -
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Residues in contact with PRO 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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290A ASN* 3.8 26.9 - - + +
291A TYR 3.7 2.0 - - - -
292A LEU* 1.3 94.5 - - + +
294A PHE* 1.3 63.5 + - - +
296A MET* 3.2 7.2 + - + +
297A GLU* 2.9 31.4 + - + +
73B PHE* 4.3 19.3 - - + +
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Residues in contact with PHE 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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291A TYR* 3.3 24.1 + + + +
292A LEU 3.3 0.2 - - - -
293A PRO* 1.3 77.6 - - - +
295A ILE* 1.3 65.6 + - + +
297A GLU* 3.3 1.8 + - - +
298A LEU* 2.9 34.9 + - + +
53B VAL* 6.3 0.2 - - + -
58B TRP* 3.5 39.9 - + - -
70B LEU* 3.4 34.1 - - + -
73B PHE* 3.9 24.4 + - + +
74B LEU* 4.1 21.1 - - + +
89B ILE* 5.7 0.7 - - + -
92B LEU* 3.8 26.0 - - + -
93B PHE* 4.3 15.0 - + - -
104B LEU* 5.6 2.5 - - + -
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Residues in contact with ILE 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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291A TYR* 2.9 27.5 + - + +
292A LEU* 2.9 12.7 + - + +
294A PHE* 1.3 80.9 - - + +
296A MET* 1.3 70.3 + - - +
298A LEU* 3.4 8.1 + - - +
299A LEU* 3.1 34.7 + - + +
49B PHE* 4.6 17.9 - - + -
53B VAL* 5.2 8.3 - - + -
103B PRO 4.7 1.3 - - - +
104B LEU* 3.5 33.9 - - + -
107B ALA* 3.5 27.4 - - + -
111B PHE* 5.0 7.0 - - + -
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Residues in contact with MET 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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292A LEU* 2.8 35.4 + - + +
293A PRO* 3.7 6.7 - - + +
295A ILE* 1.3 75.4 - - + +
297A GLU* 1.3 56.8 + - + +
299A LEU* 2.8 16.4 + - - +
300A LYS* 2.6 37.9 + - + +
111B PHE* 3.6 36.8 - - + -
116B PHE* 4.7 14.6 - - + -
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Residues in contact with GLU 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 PRO* 2.9 22.2 + - + +
294A PHE 3.8 2.0 - - - +
296A MET* 1.3 78.5 - - + +
298A LEU* 1.3 58.1 + - - +
300A LYS* 3.8 25.5 + - - +
301A THR* 2.8 34.1 + - - -
69B HIS* 3.9 12.3 + - + -
70B LEU* 3.7 16.8 - - + -
73B PHE* 3.3 46.0 - - + -
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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 PHE* 2.9 28.6 + - + +
295A ILE* 3.6 7.9 - - - +
297A GLU* 1.3 78.2 - - - +
299A LEU* 1.3 65.1 + - + +
301A THR* 3.4 2.3 + - - -
302A LEU* 3.0 57.1 + - + +
53B VAL* 4.0 30.3 - - + -
54B SER 5.9 0.4 - - - +
57B THR* 4.6 9.9 - - + -
58B TRP* 4.9 6.7 - - + -
61B VAL* 5.7 3.1 - - + -
70B LEU* 3.7 28.2 - - + +
93B PHE* 4.2 18.8 - - + -
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Residues in contact with LEU 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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295A ILE* 3.1 26.0 + - + +
296A MET* 2.8 18.2 + - - +
298A LEU* 1.3 76.5 - - + +
300A LYS* 1.3 64.8 + - - +
301A THR 3.0 1.6 - - - -
302A LEU* 2.9 22.2 + - + +
303A ALA* 2.9 14.5 + - - +
308A LEU* 4.0 27.4 - - + +
43B LEU* 4.9 17.7 - - + -
49B PHE* 5.2 8.5 - - + -
52B VAL* 5.2 1.1 - - + -
53B VAL* 4.2 21.5 - - + -
111B PHE* 5.9 3.4 - - + -
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Residues in contact with LYS 300 (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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296A MET* 2.6 19.0 + - + +
297A GLU* 3.8 26.0 + - - +
299A LEU* 1.3 71.7 - - - +
301A THR* 1.3 57.2 + - - +
303A ALA* 3.5 7.1 + - - +
304A GLU* 3.0 51.0 + - + +
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Residues in contact with THR 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 GLU* 2.8 19.7 + - - -
298A LEU* 3.5 7.4 - - - +
300A LYS* 1.3 79.2 - - - +
302A LEU* 1.3 73.9 + - + +
304A GLU* 3.2 3.0 + - - -
305A HIS* 2.2 36.4 + - - -
61B VAL* 5.7 2.0 - - + -
66B GLN* 2.2 54.6 + - + +
69B HIS* 4.6 12.6 - - - -
70B LEU* 4.6 12.2 - - + +
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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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298A LEU* 3.0 42.6 - - + +
299A LEU* 2.9 10.6 + - + +
301A THR* 1.3 83.2 - - + +
303A ALA* 1.3 58.7 + - - +
305A HIS 3.2 1.4 + - - -
306A GLN 2.9 8.3 + - - -
307A GLN* 2.9 47.8 + - + +
308A LEU* 3.2 29.9 + - + +
311A LEU* 4.2 10.8 - - + -
52B VAL* 4.7 5.4 - - + +
53B VAL* 6.4 0.4 - - + -
57B THR* 3.9 18.2 - - + -
61B VAL* 3.8 21.3 - - + -
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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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299A LEU 2.9 10.4 + - - +
300A LYS* 3.7 11.9 - - - +
302A LEU* 1.3 77.2 - - - +
304A GLU* 1.3 62.5 + - + +
305A HIS 3.1 0.7 + - - -
306A GLN* 3.1 12.7 + - - +
308A LEU* 3.6 21.6 - - + +
309A ILE* 6.4 1.3 - - - -
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Residues in contact with GLU 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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300A LYS* 3.0 42.9 + - + +
301A THR* 3.2 8.5 + - - +
303A ALA* 1.3 77.8 - - + +
305A HIS* 1.3 78.4 + - + +
306A GLN* 3.4 1.0 + - - +
66B GLN* 5.1 0.9 + - - -
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Residues in contact with HIS 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 THR 2.2 27.8 + - - -
303A ALA 3.1 0.6 - - - -
304A GLU* 1.3 101.2 + - + +
306A GLN* 1.3 70.8 + - - +
307A GLN* 2.9 36.8 + - - +
62B LEU* 4.3 9.9 - - + -
66B GLN* 2.8 45.8 + - - +
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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
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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