Contacts of the helix formed by residues 319 - 327 (chain A) in PDB entry 4XDO
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 MET 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A MET* 3.8 13.7 - - + -
298A TRP* 3.4 45.1 - - + -
299A ILE* 3.6 35.9 - - + +
302A GLY 3.9 17.0 - - - +
303A LYS* 3.9 11.9 - - + +
317A ILE 3.4 7.6 + - - +
318A SER* 1.3 73.7 + - - +
320A ASP* 1.3 67.0 + - - +
321A ILE 3.3 1.6 - - - -
322A PHE* 3.0 25.2 + - + +
323A VAL* 3.0 12.5 + - - +
334A TRP* 4.1 18.8 - - + -
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Residues in contact with ASP 320 (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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318A SER* 3.4 13.1 + - - +
319A MET* 1.3 77.8 - - - +
321A ILE* 1.3 64.4 + - - +
323A VAL* 3.0 4.0 + - - +
324A ARG* 2.9 37.2 + - - +
331A TYR* 2.4 36.3 + - - -
334A TRP* 3.7 19.8 - - + -
335A LYS* 3.6 14.4 - - - -
113B TYR* 5.4 0.5 + - - -
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Residues in contact with ILE 321 (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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162A VAL* 4.0 16.1 - - + +
166A CYS* 3.7 37.9 - - + -
168A ILE* 3.7 34.2 - - + +
318A SER* 4.2 4.4 + - - +
320A ASP* 1.3 81.7 + - - +
322A PHE* 1.3 85.2 + - + +
324A ARG* 2.8 39.9 - - - +
325A LYS* 3.0 35.3 + - + +
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Residues in contact with PHE 322 (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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158A VAL* 3.8 18.6 - - + -
159A LEU* 3.8 22.7 - - + -
162A VAL* 3.4 38.4 - - + -
168A ILE* 5.4 0.7 - - + -
170A ILE* 4.6 2.0 - - + -
298A TRP* 3.9 24.0 - + - -
299A ILE* 3.8 29.8 - - + +
317A ILE* 4.2 11.2 - - + -
318A SER 3.9 19.5 - - - -
319A MET* 3.0 19.8 + - + +
321A ILE* 1.3 88.6 - - + +
323A VAL* 1.3 58.1 + - - +
326A PHE* 3.0 40.2 + + - +
327A GLN 3.8 0.2 + - - -
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Residues in contact with VAL 323 (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 ILE* 4.3 3.1 - - + -
303A LYS* 3.6 33.7 - - + +
319A MET 3.0 13.6 + - - +
320A ASP 3.0 6.5 + - - +
322A PHE* 1.3 75.6 - - - +
324A ARG* 1.3 62.5 + - - +
327A GLN* 2.8 57.1 + - + +
330A ARG 4.5 1.3 - - - -
331A TYR* 3.7 31.1 - - + +
334A TRP* 4.0 28.0 - - + -
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Residues in contact with ARG 324 (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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320A ASP* 2.9 21.6 + - - +
321A ILE* 2.8 34.1 - - - +
323A VAL* 1.3 79.6 - - - +
325A LYS* 1.3 73.8 + - + +
328A PRO* 3.7 17.5 - - - +
331A TYR* 3.4 42.2 - - + -
112B ARG* 5.7 0.4 - - - +
113B TYR* 2.6 76.1 + - - +
114B LEU 3.5 13.3 + - - -
115B ASP* 4.9 1.0 - - - +
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Residues in contact with LYS 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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162A VAL* 5.7 1.6 - - + -
166A CYS* 4.7 9.9 - - - -
321A ILE* 3.0 33.6 + - + +
324A ARG* 1.3 87.1 - - - +
326A PHE* 1.3 81.8 + - + +
328A PRO* 3.6 12.0 - - - +
112B ARG* 4.1 14.5 - - - +
113B TYR 2.8 42.2 + - - +
114B LEU* 4.5 15.7 - - - +
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Residues in contact with PHE 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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158A VAL* 4.1 24.2 - - + -
161A VAL* 4.7 15.9 - - + -
162A VAL* 4.3 20.2 - - + -
296A VAL* 3.8 30.8 - - + +
299A ILE* 3.6 23.6 - - + -
322A PHE* 3.0 22.6 + + - +
325A LYS* 1.3 92.0 - - + +
327A GLN* 1.3 63.0 + - - +
328A PRO* 3.2 9.3 - - - +
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Residues in contact with GLN 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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296A VAL* 5.1 5.6 + - + +
299A ILE* 3.7 28.1 - - + +
300A ASP* 3.0 24.9 + - - +
303A LYS* 2.9 30.0 + - - +
322A PHE 4.7 0.2 - - - +
323A VAL* 2.8 30.5 + - + +
326A PHE* 1.3 80.0 - - + +
328A PRO* 1.3 60.4 - - - +
329A ASP* 3.1 3.4 - - - -
330A ARG* 2.8 45.0 + - + +
331A TYR 3.3 6.9 + - - -
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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