Contacts of the strand formed by residues 624 - 629 (chain C) in PDB entry 6T8O
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 ILE 624 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C HIS* 3.5 7.8 - - - -
531C SER* 4.8 16.6 - - - +
534C GLU* 4.8 4.3 - - + -
535C MET* 4.2 21.1 - - + +
538C ARG* 4.1 14.8 - - - +
590C ILE* 3.4 23.3 - - + -
592C VAL* 4.3 22.0 - - + -
615C ILE* 4.8 7.6 - - + -
619C ALA* 2.9 36.2 + - + +
622C ALA* 3.6 31.2 - - + +
623C GLY* 1.3 76.6 - - - +
625C HIS* 1.3 63.1 + - - +
626C LEU* 4.7 7.6 - - + -
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Residues in contact with HIS 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C VAL* 5.2 0.2 - - + -
456C LEU* 3.7 34.4 - - + +
457C ALA* 3.7 24.7 + - + +
460C PRO* 3.1 34.3 - - + +
461C HIS* 3.8 3.4 - - - -
589C THR* 3.6 19.9 - - + +
590C ILE 3.1 8.8 + - - +
591C VAL* 3.5 4.4 - - + +
592C VAL* 2.6 33.4 + - - +
619C ALA 5.1 0.4 - - - -
620C ARG 4.3 10.4 + - - -
623C GLY* 3.5 33.9 + - - -
624C ILE* 1.3 76.2 - - - +
626C LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C PRO 4.1 0.5 + - - +
461C HIS* 3.1 27.9 + - + +
462C LEU 2.9 25.3 + - - +
528C LEU* 5.4 2.7 - - + -
592C VAL* 3.3 35.2 - - + +
594C VAL* 4.5 4.3 - - + -
612C ILE* 4.8 15.9 - - + -
615C ILE* 3.7 29.2 - - + -
616C ALA* 6.3 1.3 - - + -
624C ILE* 4.7 3.4 - - + -
625C HIS* 1.3 84.6 - - - +
627C ILE* 1.3 67.2 + - - +
628C LEU* 3.7 38.4 - - + -
646C ILE* 5.4 1.8 - - + -
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Residues in contact with ILE 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C LEU* 5.1 3.1 - - + -
456C LEU* 3.7 29.8 - - + -
462C LEU* 3.7 27.8 - - + -
464C VAL* 4.6 8.7 - - + -
476C VAL* 4.8 14.8 - - + -
479C MET* 4.5 17.9 - - + -
480C LEU* 6.1 0.7 - - + -
591C VAL* 4.3 10.8 - - + -
592C VAL 3.0 6.6 + - - +
593C VAL* 3.4 28.2 - - + -
594C VAL* 2.8 35.1 + - - +
626C LEU* 1.3 81.7 - - - +
628C LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C LEU 3.0 13.5 + - - +
463C LEU* 3.4 13.5 - - + +
464C VAL* 2.6 37.9 + - - +
594C VAL* 3.7 24.0 - - + -
597C PHE* 3.6 30.7 - - + -
612C ILE* 4.2 21.3 - - + -
626C LEU* 3.7 27.4 - - + -
627C ILE* 1.3 75.3 - - - +
629C ALA* 1.3 53.7 + - - +
642C ILE* 4.3 5.2 - - + -
646C ILE* 3.8 29.6 - - + -
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Residues in contact with ALA 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C VAL* 3.3 19.5 - - + -
472C LYS* 4.0 13.2 - - - +
476C VAL* 4.3 17.0 - - + -
594C VAL 3.3 11.4 + - - +
595C ASP* 3.0 30.3 - - - +
596C GLU* 3.4 6.5 - - - -
597C PHE* 3.3 14.6 + - - -
627C ILE* 5.9 0.7 - - + -
628C LEU* 1.3 74.8 - - - +
630C THR* 1.3 60.4 + - - +
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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