Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 1WL4
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 PHE 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A MET* 3.8 13.2 - - + -
161A GLY* 3.6 26.5 - - - -
164A ALA* 3.5 23.3 - - + -
238A PHE* 4.2 8.5 - + - -
246A VAL* 3.8 14.4 - - + -
250A ASN 3.8 5.4 - - - +
251A ALA* 3.6 26.0 - - + +
252A SER 4.6 0.2 - - - +
293A MET* 4.6 3.6 - - + -
322A GLU 4.2 2.0 - - - -
323A ALA* 1.3 91.4 + - + +
325A ALA* 1.3 65.6 + - - +
326A ALA* 4.0 7.4 - - + +
327A VAL* 3.0 14.5 + - + +
328A SER* 3.0 22.3 + - - -
349A ILE* 4.5 4.0 - - - -
1001A COA 3.4 49.8 - - + -
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Residues in contact with ALA 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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178A GLN* 3.3 38.6 - - + +
181A VAL* 3.9 12.3 - - + +
250A ASN* 2.9 23.0 + - + +
324A PHE* 1.3 71.8 - - - +
326A ALA* 1.3 63.4 + - - +
328A SER* 3.8 2.9 - - - -
329A ALA* 2.9 27.2 + - - +
349A ILE* 3.8 19.4 - - + +
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Residues in contact with ALA 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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164A ALA* 3.8 31.0 - - + +
167A VAL* 4.0 2.6 - - - +
168A ALA* 3.9 8.1 - - + -
173A VAL* 3.7 12.1 - - - +
178A GLN* 3.6 37.2 + - - +
246A VAL* 4.7 2.5 - - + -
324A PHE* 3.2 2.3 - - + +
325A ALA* 1.3 79.2 - - - +
327A VAL* 1.3 58.2 + - - +
330A ALA* 3.2 26.3 + - - +
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Residues in contact with VAL 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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163A THR 5.5 0.2 - - - -
164A ALA* 4.1 30.7 - - + -
167A VAL* 4.2 15.3 - - + -
293A MET* 5.3 2.2 - - + -
294A GLY* 3.0 46.2 - - - +
321A ASN 5.7 3.1 - - - +
323A ALA* 5.3 1.6 - - + -
324A PHE* 3.0 20.3 + - + +
326A ALA* 1.3 76.3 - - - +
328A SER* 1.3 65.0 + - - +
330A ALA* 3.1 2.9 + - - +
331A ILE* 3.0 29.9 + - + +
383A CYS* 4.7 7.9 - - - -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 4.2 14.3 - - - +
320A ILE* 5.5 5.6 - - - +
321A ASN 5.3 3.7 + - - -
322A GLU* 4.6 20.7 + - - +
323A ALA 5.9 0.2 - - - +
324A PHE 3.0 15.2 + - - -
325A ALA* 3.8 7.6 - - - -
327A VAL* 1.3 77.6 - - - +
329A ALA* 1.3 65.7 + - - +
331A ILE* 3.3 9.2 + - - +
332A VAL* 3.1 31.9 + - - +
342A VAL* 5.4 1.2 - - - +
343A ASN* 4.5 11.2 + - - -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 3.7 26.7 - - + -
177A ASP* 5.5 1.8 - - + +
181A VAL* 4.2 19.3 - - + +
325A ALA 2.9 18.1 + - - +
328A SER* 1.3 79.3 + - - +
330A ALA* 1.3 57.4 + - - +
332A VAL* 3.4 6.3 + - - +
333A LYS* 2.9 33.3 + - - +
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Residues in contact with ALA 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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167A VAL* 3.5 24.7 - - + -
171A TRP* 3.7 29.7 - - + -
173A VAL* 4.1 3.3 - - + +
295A ILE* 4.4 5.2 - - + -
298A ILE* 4.8 1.6 - - - -
326A ALA 3.2 15.8 + - - +
327A VAL 3.1 4.5 + - - +
329A ALA* 1.3 80.9 - - - +
331A ILE* 1.3 56.8 + - - +
333A LYS* 3.8 4.0 - - - +
334A GLU* 2.9 32.6 + - - +
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Residues in contact with ILE 331 (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 GLY 3.5 25.4 - - - +
295A ILE* 4.6 3.6 - - + -
297A PRO* 3.7 26.2 - - + -
298A ILE* 4.2 23.6 - - + -
301A ILE* 4.6 0.2 - - + -
320A ILE* 3.9 36.8 - - + -
321A ASN 5.6 1.8 - - - +
327A VAL* 3.0 21.1 + - + +
328A SER* 3.7 7.0 - - - +
330A ALA* 1.3 74.1 - - - +
332A VAL* 1.3 65.8 + - - +
334A GLU* 3.4 0.5 + - - +
335A LEU* 3.0 45.7 + - + +
383A CYS* 5.7 0.2 - - + -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 5.0 3.1 - - + -
328A SER* 3.1 23.4 + - - +
329A ALA* 3.8 6.3 - - - +
331A ILE* 1.3 75.0 - - - +
333A LYS* 1.3 59.4 + - - +
336A GLY* 2.8 25.5 + - - -
337A LEU* 3.0 41.3 + - + +
339A PRO* 4.8 15.3 - - + -
342A VAL* 4.2 32.1 - - + -
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Residues in contact with LYS 333 (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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171A TRP* 2.8 38.5 + - + +
172A GLN* 3.0 22.4 + - - +
173A VAL* 4.3 10.0 - - - +
177A ASP* 4.9 3.7 + - - -
329A ALA* 2.9 18.0 + - - +
330A ALA 3.8 2.7 - - - +
332A VAL* 1.3 75.8 - - - +
334A GLU* 1.3 66.3 + - - +
336A GLY* 3.3 10.8 + - - -
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Residues in contact with GLU 334 (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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171A TRP* 3.2 25.0 + - + +
298A ILE* 3.7 35.2 - - + -
302A LYS* 5.8 2.2 + - - +
330A ALA 2.9 18.4 + - - +
333A LYS* 1.3 80.3 - - - +
335A LEU* 1.3 61.9 + - + +
336A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 335 (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 ILE* 4.0 21.5 - - + +
301A ILE* 4.0 30.5 - - + -
302A LYS* 3.8 34.5 - - + +
312A LEU* 4.0 26.1 - - + +
331A ILE* 3.0 36.6 + - + +
334A GLU* 1.3 77.7 - - + +
336A GLY* 1.3 62.2 + - - +
337A LEU* 3.6 25.3 + - + +
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Residues in contact with GLY 336 (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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313A GLU* 4.7 9.7 - - - +
332A VAL 2.8 11.3 + - - -
333A LYS* 3.3 6.7 + - - -
334A GLU 3.2 4.6 + - - -
335A LEU* 1.3 79.2 - - - +
337A LEU* 1.3 63.8 + - - +
338A ASN 3.8 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
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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