Contacts of the strand formed by residues 405 - 410 (chain B) in PDB entry 5XOU
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 ALA 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ALA 4.1 2.4 + - - -
346B LEU* 3.7 9.8 - - + +
347B ALA 2.9 23.6 + - - -
403B VAL* 3.4 4.7 - - - +
404B GLN* 1.3 80.7 - - - +
406B VAL* 1.3 65.1 + - - +
430B LEU* 4.8 0.9 - - - -
431B PRO* 3.4 13.0 - - - +
454B LEU* 4.0 19.5 - - + +
457B LYS* 4.1 9.4 - - + +
458B ALA* 3.9 23.1 - - + -
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Residues in contact with VAL 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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347B ALA* 3.2 22.7 - - + +
349B LEU* 4.0 15.0 - - + +
381B LEU* 4.2 13.5 - - + -
395B LEU* 5.2 0.4 - - + -
403B VAL* 4.4 6.3 - - + -
405B ALA* 1.3 81.0 - - - +
407B LEU* 1.3 66.4 + - - +
408B VAL* 3.7 22.0 - - + -
425B LEU* 3.9 23.1 - - + -
430B LEU* 4.5 17.5 - - + -
431B PRO 3.0 8.9 + - - +
432B SER* 3.2 2.6 - - - -
433B GLN 2.8 27.4 + - - +
454B LEU* 3.4 6.6 - - - +
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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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347B ALA 2.7 13.2 + - - +
348B LEU* 3.3 18.0 - - + +
349B LEU 2.9 24.9 + - - -
357B TRP* 3.4 30.7 - - + -
361B LEU* 3.9 21.8 - - + -
406B VAL* 1.3 71.6 - - - +
408B VAL* 1.3 60.7 + - - +
409B LEU* 4.8 4.5 - - + -
433B GLN* 3.5 30.3 - - + +
435B LEU* 4.3 20.9 - - + -
450B ALA* 4.9 3.4 - - + +
451B LEU* 4.5 9.0 - - + -
454B LEU* 3.7 23.8 - - + +
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Residues in contact with VAL 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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349B LEU* 3.3 18.6 - - + +
351B LEU* 4.0 29.6 - - + -
406B VAL* 3.7 19.3 - - + -
407B LEU* 1.3 76.3 - - - +
409B LEU* 1.3 61.1 + - - +
410B THR* 3.7 10.8 + - + +
421B LEU* 4.0 15.0 - - + -
425B LEU* 4.4 4.0 - - + -
432B SER* 4.1 18.8 - - - -
433B GLN 2.8 14.2 + - - +
434B ILE* 3.5 11.1 - - + -
435B LEU 2.9 28.5 + - - +
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Residues in contact with LEU 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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348B LEU* 3.9 16.4 - - + -
349B LEU 3.0 7.7 + - - +
350B ARG* 3.6 40.3 - - - +
351B LEU* 2.8 28.1 + - - +
352B ASP* 3.9 3.4 + - - +
358B PRO* 3.7 31.0 - - + -
361B LEU* 4.8 4.9 - - + -
407B LEU* 3.8 4.0 + - + -
408B VAL* 1.3 68.5 - - - +
410B THR* 1.3 61.1 + - - +
435B LEU* 3.5 40.4 - - + +
437B VAL* 4.4 19.1 - - + -
439B LEU* 4.7 5.2 - - + -
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Residues in contact with THR 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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351B LEU* 3.8 21.8 - - - +
408B VAL* 4.0 8.1 - - + +
409B LEU* 1.3 77.0 - - - +
411B PRO* 1.3 95.2 + - - +
413B MET* 3.5 23.1 - - + +
434B ILE* 3.7 29.8 - - + -
435B LEU 3.4 3.2 + - - -
436B ASN* 3.1 11.7 - - - +
437B VAL* 2.9 24.4 + - - +
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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