Contacts of the helix formed by residues 317 - 325 (chain A) in PDB entry 6DXW
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 SER 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A TYR* 3.8 17.9 - - - -
315A ASN 3.4 4.4 + - - -
316A LEU* 1.3 77.2 - - - +
318A LEU* 1.3 60.0 + - - +
319A GLU* 3.5 8.8 + - - +
320A ALA* 3.0 23.0 + - - +
321A LEU* 2.9 30.7 + - - +
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Residues in contact with LEU 318 (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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139A TYR* 3.7 30.8 - - + -
140A HIS 4.2 2.5 - - - +
317A SER* 1.3 73.4 - - - +
319A GLU* 1.3 57.8 + - - +
321A LEU* 3.2 7.3 + - + +
322A PHE* 2.9 28.1 + - - +
340A VAL* 3.7 20.7 - - + +
341A MET 3.4 44.4 - - - +
342A SER* 4.4 6.3 - - - -
348A LYS* 3.5 48.0 - - + +
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Residues in contact with GLU 319 (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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317A SER* 3.2 8.3 + - - +
318A LEU* 1.3 78.7 - - - +
320A ALA* 1.3 63.2 + - - +
322A PHE* 3.1 14.7 + - - +
323A GLN* 2.8 54.4 + - + +
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Residues in contact with ALA 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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311A THR* 4.0 17.4 + - + +
315A ASN 3.6 19.1 - - - +
316A LEU* 4.5 1.8 - - + -
317A SER* 3.0 25.0 + - - +
319A GLU* 1.3 77.1 - - - +
321A LEU* 1.3 57.1 + - - +
323A GLN* 3.3 9.0 + - - +
324A ILE* 2.9 34.2 + - + +
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Residues in contact with LEU 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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129A ILE* 3.7 35.4 - - + +
131A ALA* 5.1 1.3 - - + -
139A TYR* 3.8 14.4 - - + +
140A HIS* 3.6 19.1 - - - +
141A GLY* 3.6 27.6 - - - +
308A LEU* 4.2 9.9 - - + -
316A LEU* 4.2 18.6 - - + +
317A SER 2.9 14.2 + - - +
318A LEU* 3.2 12.5 + - + +
320A ALA* 1.3 73.9 - - - +
322A PHE* 1.3 59.4 + - - +
324A ILE* 3.2 8.1 + - + +
325A LEU* 2.8 38.1 + - + +
340A VAL* 4.3 6.1 - - + -
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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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30A PRO* 3.9 21.3 - - + -
318A LEU 2.9 13.7 + - - +
319A GLU* 3.1 19.5 + - - +
321A LEU* 1.3 74.8 - - - +
323A GLN* 1.3 79.4 + - - +
325A LEU* 3.3 7.0 + - - +
326A SER* 2.8 37.2 + - - -
338A THR* 3.6 24.9 - - + -
340A VAL* 4.0 18.1 - - + +
350A MET* 6.4 0.4 - - + -
352A ARG* 3.9 29.8 - - + -
354A ARG* 3.5 29.3 + - - -
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Residues in contact with GLN 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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319A GLU* 2.8 43.3 + - + +
320A ALA* 3.6 9.9 - - - +
321A LEU 3.2 0.4 - - - -
322A PHE* 1.3 92.4 - - - +
324A ILE* 1.3 65.5 + - + +
326A SER* 3.1 20.9 + - - -
327A VAL* 3.4 14.0 - - - +
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Residues in contact with ILE 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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129A ILE* 3.8 23.8 - - + -
304A ALA* 4.2 13.2 - - + +
307A ALA* 3.8 23.5 - - + +
308A LEU* 3.7 31.0 - - + -
311A THR* 3.5 28.7 - - + +
316A LEU* 5.4 1.3 - - + -
320A ALA* 2.9 24.3 + - + +
321A LEU* 3.5 13.2 - - + +
323A GLN* 1.3 75.5 - - + +
325A LEU* 1.3 59.2 + - - +
326A SER 3.1 4.2 + - - -
327A VAL* 3.2 25.3 + - - +
330A VAL* 4.2 8.6 - - + +
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Residues in contact with LEU 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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127A THR* 4.1 9.4 - - + +
129A ILE* 4.1 24.2 - - + -
141A GLY* 3.7 12.1 - - - -
142A ARG* 3.4 24.7 - - - +
143A ASN* 2.7 57.0 + - - +
321A LEU* 2.8 25.0 + - + +
322A PHE 3.3 5.6 + - - +
323A GLN 3.2 0.2 - - - -
324A ILE* 1.3 74.6 - - - +
326A SER* 1.3 57.3 + - - +
327A VAL 3.4 0.9 - - - -
330A VAL* 4.1 14.4 - - + -
331A TYR* 3.3 7.7 - - - +
338A THR* 3.9 19.1 - - + -
339A THR 4.4 0.9 - - - +
340A VAL* 4.5 2.0 - - + -
354A ARG* 4.1 4.5 + - - -
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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
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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