Contacts of the helix formed by residues 320 - 328 (chain A) in PDB entry 4X61
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 GLU 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ASN 3.7 4.4 + - - +
319A LEU* 1.3 78.5 - - - +
321A SER* 1.3 67.4 + - - +
322A GLN* 3.3 5.6 - - + +
323A THR* 3.2 27.7 + - - +
324A TYR* 3.4 10.4 - - - -
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Residues in contact with SER 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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320A GLU* 1.3 74.5 - - - +
322A GLN* 1.3 65.4 + - - +
324A TYR* 3.4 13.4 + - - +
325A GLU* 3.2 19.0 + - - +
368A ARG* 3.7 21.7 + - - +
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Residues in contact with GLN 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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320A GLU* 3.3 4.4 - - + +
321A SER* 1.3 80.0 - - - +
323A THR* 1.3 66.1 + - - +
325A GLU* 3.5 23.6 - - - +
326A VAL* 3.0 32.1 + - + +
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Residues in contact with THR 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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312A LEU* 6.5 0.2 - - + -
319A LEU* 3.9 24.8 - - + +
320A GLU* 3.2 31.3 + - - +
322A GLN* 1.3 76.7 - - - +
324A TYR* 1.3 66.8 + - - +
326A VAL* 3.3 3.5 + - - +
327A PHE* 3.1 49.2 + - + -
702A 3XV 4.4 4.7 - - + -
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Residues in contact with TYR 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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319A LEU* 3.7 27.9 - - + +
320A GLU 3.4 17.5 + - - -
321A SER* 3.4 8.5 + - - +
323A THR* 1.3 76.7 - - - +
325A GLU* 1.3 63.5 + - - +
327A PHE* 3.2 3.5 + - - +
328A GLU* 2.9 41.7 + - - +
367A GLY* 3.7 13.0 - - - -
368A ARG* 3.6 24.0 - - + +
394A ASN* 2.9 37.7 + - - +
397A ALA* 3.9 15.8 - - + +
701A SAM 2.6 36.6 + - + -
702A 3XV 4.0 23.0 - + - -
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Residues in contact with GLU 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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321A SER* 3.2 9.2 + - - +
322A GLN* 3.5 29.8 - - - +
323A THR 3.2 0.4 - - - -
324A TYR* 1.3 80.5 - - - +
326A VAL* 1.3 65.1 + - + +
328A GLU* 3.4 19.4 + - - +
329A LYS* 3.6 32.7 + - - +
368A ARG* 3.5 18.4 + - - +
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Residues in contact with VAL 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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300A PHE* 5.4 5.8 - - + -
304A TYR* 5.7 0.9 - - - +
322A GLN* 3.0 24.3 + - + +
323A THR* 3.3 5.6 + - - +
325A GLU* 1.3 80.2 - - + +
327A PHE* 1.3 70.8 + - + +
329A LYS* 3.2 29.6 + - + +
577A PHE* 3.6 11.2 - - + -
702A 3XV 4.0 28.9 - - + +
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Residues in contact with PHE 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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323A THR* 3.1 38.7 + - + +
324A TYR 3.2 4.0 + - - +
326A VAL* 1.3 77.2 - - + +
328A GLU* 1.3 60.1 + - - +
329A LYS 3.1 5.7 + - - -
330A ASP* 3.5 13.1 + - - +
333A LYS* 4.7 0.3 + - - -
334A TYR* 3.2 17.8 + - - -
577A PHE* 4.5 6.5 - + - -
578A SER* 3.1 37.5 + - - +
702A 3XV 3.5 109.0 - + + -
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Residues in contact with GLU 328 (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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324A TYR* 2.9 24.5 + - - +
325A GLU* 3.5 8.3 - - - +
326A VAL 3.2 0.4 - - - -
327A PHE* 1.3 75.2 - - - +
329A LYS* 1.3 57.7 + - + +
330A ASP 3.2 6.8 + - - +
334A TYR* 3.4 28.7 - - + +
368A ARG* 2.8 64.3 + - - +
370A PRO* 4.1 16.1 - - + +
701A SAM 4.1 8.0 - - - +
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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