Contacts of the strand formed by residues 668 - 672 (chain B) in PDB entry 5IXC
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 LEU 668 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B VAL 3.2 3.5 + - - +
323B VAL* 3.4 20.6 - - + +
324B GLY 3.0 24.4 + - - -
666B LEU* 4.0 0.9 - - - +
667B ASP* 1.3 82.4 - - - +
669B ILE* 1.3 71.7 + - - +
670B LEU* 4.4 17.3 - - + -
726B ILE* 3.4 37.9 - - + +
727B LEU 4.4 0.2 - - - +
728B LEU* 4.5 5.8 - - + +
796B ILE* 4.6 1.8 - - + +
799B ALA* 3.9 23.3 - - + +
800B LEU* 3.8 34.3 - - + +
803B ALA* 4.2 11.2 - - + -
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Residues in contact with ILE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLY 3.5 6.5 - - - +
326B MET* 3.7 42.6 - - + -
659B MET* 4.2 13.9 - - + -
660B PHE* 3.9 31.6 - - + -
666B LEU* 3.8 21.5 - - + -
668B LEU* 1.3 77.6 - - - +
670B LEU* 1.3 68.5 + - - +
671B SER* 3.5 1.5 + - - +
697B PHE* 5.0 5.6 - - + -
725B PRO* 4.0 16.4 - - + -
726B ILE 2.8 12.6 + - - +
727B LEU* 3.6 10.9 - - + +
728B LEU 3.0 27.0 + - - +
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Residues in contact with LEU 670 (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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323B VAL* 4.6 16.2 - - + -
324B GLY 2.9 14.5 + - - +
325B ILE* 3.5 12.3 - - + +
326B MET 2.9 27.7 + - - +
345B LEU* 4.1 35.0 - - + -
354B VAL* 4.8 4.5 - - + -
668B LEU* 4.4 14.8 - - + -
669B ILE* 1.3 73.0 - - - +
671B SER* 1.3 60.6 + - - +
672B PHE* 3.7 15.9 + - + -
728B LEU* 3.5 33.2 - - + -
730B PHE* 4.4 8.7 - - + -
796B ILE* 4.6 13.9 - - + -
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Residues in contact with SER 671 (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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326B MET* 3.3 34.4 + - - +
328B THR* 6.1 0.2 - - - +
654B THR* 5.0 3.6 + - - +
669B ILE* 3.5 0.4 + - - -
670B LEU* 1.3 71.1 - - - +
672B PHE* 1.3 63.0 + - - +
683B LEU* 4.0 2.6 - - - +
727B LEU* 3.6 13.5 - - - -
728B LEU 2.7 15.4 + - - -
729B HIS* 3.0 26.9 + - - -
730B PHE* 2.8 29.8 + - - -
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Residues in contact with PHE 672 (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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325B ILE* 3.6 39.9 - - + -
326B MET 2.8 15.2 + - - +
327B ALA* 3.5 1.9 - - + -
328B THR* 3.4 24.6 + - - +
338B LEU* 4.2 7.6 - - + -
341B HIS* 3.5 27.1 - + + +
342B LEU* 5.6 0.7 - - + -
345B LEU* 4.1 22.4 - - + -
654B THR* 4.7 0.5 + - - -
670B LEU* 4.3 13.9 - - + -
671B SER* 1.3 74.9 + - - +
673B ASP* 1.3 60.8 + - - +
674B TYR* 3.3 27.8 - - + +
730B PHE* 3.5 40.2 - + + -
789B VAL* 3.8 17.5 - - + -
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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