Contacts of the helix formed by residues 300 - 311 (chain A) in PDB entry 6XYU
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 ASN 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 5.9 0.2 - - - -
296A MET* 2.8 25.6 + - + +
299A THR* 1.3 81.5 + - - +
301A PRO* 1.3 66.1 - - - +
302A ALA* 3.3 19.2 + - - +
303A HIS* 3.3 26.4 + - + +
304A VAL* 3.6 14.2 + - - +
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Residues in contact with PRO 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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194A MET* 3.7 23.8 - - + -
195A PRO* 4.1 7.2 - - + -
198A PHE* 3.6 39.5 - - + -
297A LEU* 3.1 31.2 - - + +
298A LYS 3.8 9.2 - - - +
299A THR 3.9 1.3 - - - +
300A ASN* 1.3 86.7 - - - +
302A ALA* 1.3 68.0 + - - +
304A VAL* 3.0 4.6 + - + +
305A MET* 2.9 27.6 + - + +
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Residues in contact with ALA 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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198A PHE* 4.1 20.8 - - + -
201A GLU* 5.1 4.5 - - - +
300A ASN* 3.3 9.0 + - - +
301A PRO* 1.3 79.8 - - - +
303A HIS* 1.3 58.7 + - - +
305A MET* 3.3 7.2 + - - +
306A SER* 2.8 33.0 + - - +
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Residues in contact with HIS 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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293A ASN* 5.5 4.0 - - - -
296A MET* 3.3 26.5 - - + +
300A ASN* 3.3 28.8 + - - +
301A PRO 3.1 0.8 - - - -
302A ALA* 1.3 76.9 - - - +
304A VAL* 1.3 64.0 + - - +
306A SER* 3.3 10.3 + - - -
307A CYS* 3.0 32.3 + - + +
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Residues in contact with VAL 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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287A ILE* 3.6 32.5 - - + -
292A CYS* 4.0 10.7 - - - +
294A ALA* 4.4 1.6 - - - +
296A MET* 3.6 48.0 - - + +
297A LEU* 3.8 24.9 - - + +
300A ASN 3.6 7.8 + - - +
301A PRO 3.0 7.2 + - - +
303A HIS* 1.3 77.4 - - - +
305A MET* 1.3 58.4 + - - +
307A CYS* 3.5 8.6 - - - +
308A MET* 3.1 25.9 + - + +
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Residues in contact with MET 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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44A PHE* 3.9 26.5 - - + -
188A LEU* 4.6 0.7 - - + -
190A LEU* 3.9 23.3 - - + -
194A MET* 4.2 10.3 - - - -
201A GLU* 3.2 45.5 - - + +
202A ALA* 4.2 7.6 - - + -
287A ILE* 5.2 1.3 - - - -
297A LEU* 4.4 9.0 - - - -
301A PRO* 2.9 21.9 + - + +
302A ALA 3.7 4.3 - - - +
304A VAL* 1.3 79.2 - - - +
306A SER* 1.3 65.0 + - - +
308A MET* 3.2 5.9 + - + +
309A ARG* 2.9 46.6 + - - +
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Residues in contact with SER 306 (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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302A ALA* 2.8 18.7 + - - +
303A HIS* 3.6 13.1 - - - -
305A MET* 1.3 74.8 - - - +
307A CYS* 1.3 60.0 + - - +
309A ARG* 2.9 18.5 + - - +
310A SER* 2.8 25.2 + - - -
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Residues in contact with CYS 307 (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 ASN 3.7 6.5 - - - -
292A CYS* 2.1 53.0 - - + +
303A HIS* 3.0 23.3 + - + +
304A VAL* 3.5 10.5 - - - +
305A MET 3.2 0.2 - - - -
306A SER* 1.3 75.3 - - - +
308A MET* 1.3 54.2 + - - +
310A SER* 3.1 22.1 + - - -
311A VAL* 3.2 16.9 + - - +
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Residues in contact with MET 308 (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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43A ARG* 2.8 22.7 + - - -
44A PHE* 3.9 26.2 - - + -
188A LEU* 4.8 2.0 - - + -
286A LEU* 3.9 34.5 - - + -
287A ILE* 3.7 42.2 - - + -
290A CYS* 3.9 19.3 - - - -
292A CYS* 3.9 14.4 - - - -
304A VAL 3.1 20.2 + - - +
305A MET* 3.2 11.6 + - + +
307A CYS* 1.3 74.4 - - - +
309A ARG* 1.3 59.3 + - - +
311A VAL* 3.8 9.3 + - - +
316A ILE* 3.9 12.0 - - + +
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Residues in contact with ARG 309 (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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40A GLU* 3.1 33.4 - - - +
41A ASP* 3.0 28.6 + - - +
43A ARG* 2.1 59.4 + - + +
44A PHE* 4.3 3.2 - - + -
45A ARG* 3.4 8.7 - - - +
201A GLU* 2.1 54.1 + - - +
305A MET* 2.9 28.6 + - - +
306A SER* 2.9 9.3 + - - +
308A MET* 1.3 77.5 - - - +
310A SER* 1.3 60.5 + - - +
311A VAL 3.4 1.0 - - - +
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Residues in contact with SER 310 (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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306A SER* 2.8 18.1 + - - -
307A CYS* 3.1 9.7 + - - -
309A ARG* 1.3 77.2 - - - +
311A VAL* 1.3 63.7 + - - +
312A ASP* 3.5 5.4 + - - +
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Residues in contact with VAL 311 (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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43A ARG* 2.8 25.9 + - - +
290A CYS* 3.8 30.1 - - + +
292A CYS* 4.0 7.0 - - - -
307A CYS* 3.2 16.1 + - - +
308A MET* 3.8 12.8 - - - +
309A ARG 3.4 1.3 - - - +
310A SER* 1.3 78.5 - - - +
312A ASP* 1.3 76.9 + - - +
315A THR* 3.5 25.6 - - + -
316A ILE* 3.8 15.0 - - + -
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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