Contacts of the strand formed by residues 440 - 445 (chain F) in PDB entry 6T8G
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 PRO 440 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432F TYR* 3.6 28.3 - - + -
435F HIS* 4.2 21.3 - - + +
437F SER 4.8 1.8 - - - +
438F THR 3.6 8.5 - - - +
439F VAL* 1.3 88.9 - - - +
441F LEU* 1.3 63.2 + - - +
442F ALA 4.0 0.2 - - - -
453F ILE* 4.2 18.8 - - + -
454F THR 4.2 1.8 - - - +
455F ASP* 4.1 8.1 - - - +
482F SER* 3.9 14.1 - - - +
483F ILE* 3.3 19.7 - - + +
486F LYS* 4.2 19.1 - - + -
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Residues in contact with LEU 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439F VAL 4.0 0.4 + - - -
440F PRO* 1.3 83.0 - - - +
442F ALA* 1.3 60.0 + - - +
443F LEU* 3.4 8.9 + - + +
453F ILE* 3.3 4.3 - - - +
454F THR* 2.9 49.4 + - - +
456F LEU* 3.8 18.6 - - + -
459F MET* 3.7 30.1 - - + -
462F LEU* 4.1 3.6 - - + -
479F MET* 3.5 62.4 - - + +
482F SER* 4.1 0.2 - - - -
483F ILE* 4.0 11.0 - - + -
627F ILE* 4.8 1.1 - - + -
650F ILE* 6.1 0.7 - - + -
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Residues in contact with ALA 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F PHE* 4.2 12.0 - - + -
426F VAL* 4.2 5.2 - - + +
427F LEU* 3.7 26.0 - - + -
432F TYR* 4.3 3.8 - - + -
440F PRO 4.0 0.4 - - - -
441F LEU* 1.3 70.0 - - - +
443F LEU* 1.3 66.8 + - - +
453F ILE* 3.7 28.3 - - + -
478F ALA* 4.5 6.7 - - - +
479F MET* 5.6 0.6 - - - +
482F SER* 3.2 29.8 + - - +
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Residues in contact with LEU 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F VAL* 3.4 9.9 - - - +
441F LEU* 3.4 11.5 + - + +
442F ALA* 1.3 79.9 - - - +
444F GLY* 1.3 67.1 + - - +
451F PRO* 4.1 1.4 - - - +
452F ILE 3.7 23.3 + - - +
453F ILE* 4.3 0.5 - - - +
454F THR* 4.4 10.3 - - + +
475F GLY* 5.4 3.1 - - - +
478F ALA* 5.5 6.7 - - + -
479F MET* 3.9 28.9 - - + -
650F ILE* 4.0 15.5 - - + -
678F MET* 3.7 37.7 - - + -
680F TYR* 4.1 16.8 - - + -
691F VAL* 3.8 14.4 - - + -
693F GLY* 5.5 1.8 - - - -
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Residues in contact with GLY 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F VAL* 4.6 0.7 - - - -
426F VAL* 3.7 22.4 - - - -
442F ALA 4.0 0.2 + - - -
443F LEU* 1.3 81.2 - - - +
445F HIS* 1.3 66.8 + - - -
451F PRO* 3.9 4.9 - - - -
452F ILE 3.1 15.1 + - - -
691F VAL* 3.3 5.7 - - - +
692F HIS 3.2 18.7 + - - -
693F GLY* 4.5 0.4 - - - -
694F ALA* 4.5 9.8 - - - +
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Residues in contact with HIS 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F PRO* 4.9 11.4 - - + -
421F VAL* 3.5 34.0 - - + +
422F ARG 5.2 0.8 + - - -
425F GLU* 3.5 32.0 + - + +
426F VAL* 4.3 2.2 - - + +
444F GLY* 1.3 74.6 - - - -
446F ASP* 1.3 67.7 + - - +
449F GLY* 4.1 6.7 - - - -
450F ARG* 3.3 16.7 + - - +
451F PRO* 3.2 32.6 - - + -
691F VAL* 3.4 1.8 - - - +
692F HIS* 2.7 41.8 + - + +
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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