Contacts of the strand formed by residues 617 - 623 (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 LEU 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B VAL* 3.8 19.7 - - + -
574B ARG 3.7 12.3 - - - +
575B LYS* 4.0 5.8 - - - -
602B LEU* 3.2 7.4 - - - +
603B LEU* 2.9 36.5 + - + +
605B THR* 4.3 12.8 - - + +
615B ARG 3.5 0.6 + - - -
616B PRO* 1.3 74.2 - - - +
618B LYS* 1.3 59.8 + - - +
619B LEU* 3.6 18.1 - - + +
635B ILE* 5.5 0.7 - - + -
651B ARG* 3.4 59.9 - - + +
652B LEU* 4.2 15.7 - - + -
653B PRO* 4.5 7.2 - - + -
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Residues in contact with LYS 618 (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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574B ARG* 2.8 67.1 + - + +
576B SER 5.2 0.2 - - - +
577B GLY* 3.4 23.5 + - - +
578B GLY* 3.7 18.8 - - - +
596B LEU* 6.0 2.7 - - + -
600B THR* 3.8 27.4 - - + -
601B PHE 3.8 2.0 - - - -
602B LEU* 4.1 11.4 - - + -
616B PRO 3.8 0.8 + - - -
617B LEU* 1.3 73.4 - - - +
619B LEU* 1.3 62.3 + - - +
620B VAL* 4.9 3.1 - - - +
8F C 3.0 25.1 + - - +
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Residues in contact with LEU 619 (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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571B VAL* 3.8 10.1 - - + -
572B SER 3.2 7.2 - - - +
573B VAL* 3.9 17.3 - - + -
599B LYS 3.9 0.3 - - - +
600B THR* 3.3 5.2 - - - +
601B PHE* 2.9 63.4 + - + +
603B LEU* 3.6 23.8 - - + -
617B LEU* 3.6 26.7 - - + +
618B LYS* 1.3 78.7 - - - +
620B VAL* 1.3 65.3 + - - +
621B HIS 4.2 0.2 - - - -
635B ILE* 3.6 41.5 - - + -
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Residues in contact with VAL 620 (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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571B VAL* 3.5 4.1 - - - -
572B SER* 2.9 35.5 + - - -
574B ARG* 3.8 34.8 - - - +
599B LYS* 3.4 11.2 - - + +
600B THR* 4.3 20.9 - - + +
618B LYS* 4.9 3.1 - - - +
619B LEU* 1.3 80.1 - - - +
621B HIS* 1.3 64.8 - - - +
622B GLU* 3.2 31.2 + - - +
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Residues in contact with HIS 621 (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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569B ASP* 3.0 16.6 + - - -
570B LEU 3.4 9.0 - - - -
571B VAL* 4.3 6.0 - - + +
599B LYS* 2.8 46.3 + - + +
601B PHE* 5.5 2.1 - - + -
619B LEU 4.2 0.8 - - - -
620B VAL* 1.3 71.2 - - - +
622B GLU* 1.3 60.8 + - - +
623B ALA 3.0 28.8 + - - -
624B GLY 3.3 20.2 + - - -
626B THR 3.2 25.4 + - - -
628B LEU* 3.4 27.1 - - + +
631B LEU* 3.3 24.1 - - + +
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Residues in contact with GLU 622 (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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549B VAL* 4.6 20.3 - - + +
570B LEU* 2.8 35.4 + - + +
571B VAL 5.0 0.2 - - - +
572B SER* 3.6 17.9 - - - +
574B ARG* 5.4 3.8 + - - -
620B VAL* 3.2 30.8 + - - +
621B HIS* 1.3 73.8 - - - +
623B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 623 (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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558B LEU* 3.6 30.3 - - + -
568B TYR* 3.9 8.1 - - + +
569B ASP* 3.3 1.0 - - - -
570B LEU* 2.7 34.1 + - + +
599B LYS* 6.1 0.4 - - - +
621B HIS* 3.0 10.7 + - - -
622B GLU* 1.3 81.9 - - - +
624B GLY* 1.3 61.4 + - - +
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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