Contacts of the helix formed by residues 405 - 411 (chain B) in PDB entry 2XFN
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 GLY 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.7 24.0 - - - -
179A GLU* 4.5 4.4 - - - +
144B ASP* 2.9 32.4 + - - +
145B ASN* 4.1 2.9 - - - -
403B PRO 3.3 0.4 + - - -
404B PRO* 1.3 71.8 - - - +
406B ILE* 1.3 63.2 + - - +
408B THR* 3.7 1.1 + - - -
409B GLN* 3.3 27.4 + - - +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 4.5 7.4 - - + +
401A TYR* 4.0 16.2 - - - +
144B ASP* 3.5 0.2 + - - -
288B ARG* 3.9 50.5 - - + +
289B VAL* 4.3 2.9 - - + -
402B PHE* 3.7 22.7 - - + -
403B PRO* 3.3 32.1 + - + +
404B PRO 3.9 6.3 - - - +
405B GLY* 1.3 81.1 - - - +
407B LEU* 1.3 58.9 + - - +
408B THR 3.3 0.4 - - - -
409B GLN 3.2 0.2 + - - -
410B TYR* 2.7 49.4 + - + +
411B GLY 3.7 0.2 + - - -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PRO* 3.9 25.8 - - + -
135B TRP* 4.1 18.8 - - + +
144B ASP* 3.4 12.7 + - - +
183B LEU* 3.9 19.3 - - + -
184B TRP* 3.6 37.2 - - + -
187B TRP* 4.9 2.0 - - + -
402B PHE* 3.6 39.6 - - + +
406B ILE* 1.3 78.4 - - - +
408B THR* 1.3 59.5 + - - +
411B GLY* 2.8 36.3 + - - -
414B LEU* 6.0 1.6 - - + -
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Residues in contact with THR 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TRP* 4.1 11.0 - - + +
140B ALA* 3.7 26.7 - - + +
141B GLU* 4.2 16.1 + - + +
144B ASP* 2.6 41.1 + - + +
145B ASN* 4.8 2.9 + - - -
183B LEU* 3.7 12.8 - - + -
405B GLY* 3.7 6.2 + - - -
407B LEU* 1.3 79.6 - - - +
409B GLN* 1.3 70.7 + - - +
411B GLY 4.6 0.9 + - - -
412B ARG* 3.8 21.1 + - - -
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 6.1 2.0 - - - +
179A GLU* 4.9 0.9 - - - +
347A HIS* 3.5 22.3 - - - +
350A ARG* 3.0 46.4 + - - +
141B GLU* 4.6 12.7 + - - -
281B MET* 3.1 22.2 - - - +
405B GLY 3.3 19.5 + - - +
406B ILE 3.2 1.4 + - - -
408B THR* 1.3 87.4 + - - +
410B TYR* 1.3 77.5 + - + +
412B ARG* 5.9 0.9 + - - +
413B VAL* 5.1 0.2 - - - +
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.2 26.9 + - - -
281B MET* 3.5 48.5 - - + -
284B GLN* 3.0 33.4 + - + -
285B MET* 3.8 27.2 - - + +
288B ARG* 3.3 36.2 + - - -
402B PHE* 5.4 1.3 - - + -
406B ILE* 2.7 32.5 + - + +
409B GLN* 1.3 91.7 - - + +
411B GLY* 1.3 62.8 + - - +
412B ARG* 3.2 3.4 - - - -
413B VAL* 3.0 25.7 + - - +
414B LEU* 4.0 2.4 + - - +
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Residues in contact with GLY 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TRP* 3.5 24.2 - - - -
402B PHE* 4.7 6.3 - - - -
406B ILE 3.7 0.8 + - - -
407B LEU* 2.8 38.8 + - - -
408B THR 4.5 0.4 - - - -
409B GLN 3.9 0.6 - - - -
410B TYR* 1.3 71.6 - - - +
412B ARG* 1.3 62.7 + - - +
413B VAL 3.2 0.9 + - - -
414B LEU* 3.2 22.1 + - - +
415B ARG 4.9 0.2 + - - -
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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