Contacts of the strand formed by residues 505 - 520 (chain C) in PDB entry 3A8P
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 VAL 505 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C VAL* 1.3 82.5 - - - +
506C ARG* 1.3 62.4 + - - +
507C LYS* 3.5 28.0 - - - +
508C ALA* 4.0 13.5 - - + -
539C THR* 4.4 17.5 - - + +
540C LEU 3.5 8.3 - - - +
541C LYS* 4.7 10.1 - - + +
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Residues in contact with ARG 506 (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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504C VAL* 3.1 7.2 + - + +
505C VAL* 1.3 74.3 - - - +
507C LYS* 1.3 63.9 + - - +
540C LEU* 2.9 23.4 + - + +
542C GLY 5.0 4.0 + - - +
612C ALA* 3.4 31.6 - - + +
615C SER* 3.3 22.4 - - - -
616C ALA* 3.9 29.1 - - - +
619C SER* 4.5 10.9 - - - -
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Residues in contact with LYS 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 3.4 5.2 - - - +
506C ARG* 1.3 84.1 - - - +
508C ALA* 1.3 76.8 + - - +
509C GLY* 5.2 0.4 - - - -
539C THR* 3.3 1.6 - - - -
540C LEU* 2.7 36.3 + - + +
605C ASP* 3.1 23.4 + - - -
608C ASN* 3.5 42.2 - - + +
609C TRP* 3.4 38.3 - - + +
612C ALA* 3.8 18.6 - - + -
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Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 4.0 14.8 - - + +
507C LYS* 1.3 92.6 + - - +
509C GLY* 1.3 58.4 + - - +
537C TRP* 3.7 21.2 - - + -
538C VAL 3.1 11.7 - - - +
539C THR* 4.0 9.6 - - + -
609C TRP* 3.9 6.1 - - - -
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Residues in contact with GLY 509 (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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507C LYS* 5.2 0.9 - - - -
508C ALA* 1.3 76.7 - - - +
510C TRP* 1.3 64.6 + - - -
511C LEU 3.7 0.3 + - - -
537C TRP* 3.3 23.6 - - - -
538C VAL* 2.9 32.1 + - - +
605C ASP* 6.0 0.4 - - - -
609C TRP* 3.8 10.4 - - - -
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Residues in contact with TRP 510 (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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509C GLY* 1.3 72.8 - - - -
511C LEU* 1.3 69.7 + - - +
535C GLN* 3.5 41.5 - - + +
536C TYR* 3.4 23.6 - - - -
537C TRP* 3.6 39.6 - + + -
549C GLU 4.2 8.3 - - - -
550C THR* 4.1 8.7 - - + -
551C TYR* 3.8 39.3 - - + +
599C GLN 4.4 0.9 - - - +
601C THR* 4.0 27.8 - - + +
605C ASP* 4.4 2.6 - - - +
609C TRP* 4.8 0.2 + - - -
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Residues in contact with LEU 511 (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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509C GLY 4.3 0.9 - - - +
510C TRP* 1.3 81.5 - - - +
512C PHE* 1.3 70.6 + - - +
513C PHE* 3.8 1.4 + - + +
535C GLN* 3.5 1.7 - - - +
536C TYR* 2.9 33.1 + - - +
538C VAL* 3.9 24.7 - - + -
545C LEU* 6.1 0.9 - - + -
586C PHE* 3.9 12.8 - - + -
598C PHE* 3.8 22.9 - - + -
599C GLN 3.6 16.4 - - - +
600C ALA* 3.8 9.9 - - - -
605C ASP* 4.5 0.2 - - - +
609C TRP* 3.4 56.1 - - + +
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Residues in contact with PHE 512 (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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511C LEU* 1.3 76.1 - - - +
513C PHE* 1.3 60.5 + - - +
533C TRP* 3.8 33.0 - - + -
534C LYS 3.4 4.7 - - - -
535C GLN* 3.7 51.8 - - + -
582C LYS* 5.9 1.6 - - - -
598C PHE* 3.2 8.5 - - - +
599C GLN* 2.9 60.0 + - + +
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Residues in contact with PHE 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C LEU* 4.8 1.8 - - + +
512C PHE* 1.3 76.7 - - - +
514C LYS* 1.3 69.3 + - - +
515C PRO* 3.9 19.2 - - + +
532C LYS 3.6 1.7 - - - +
533C TRP* 3.4 2.4 - - - -
534C LYS* 2.6 39.5 + - + +
536C TYR* 4.0 20.2 - + + -
547C PHE* 3.6 29.6 - + + -
564C CYS* 5.9 4.9 - - - -
566C LEU* 4.5 2.9 - - + -
596C TYR* 3.5 46.9 - + + -
597C LEU 3.5 4.7 - - - -
598C PHE* 3.4 28.0 - + + -
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Residues in contact with LYS 514 (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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513C PHE* 1.3 82.6 - - - +
515C PRO* 1.3 70.1 - - + +
516C LEU* 5.7 0.4 - - + -
531C ARG* 3.4 37.8 + - + +
532C LYS* 3.6 24.4 - - - +
533C TRP* 3.0 56.1 - - + +
579C HIS* 5.7 1.4 + - - -
597C LEU* 2.8 48.4 + - + +
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Residues in contact with PRO 515 (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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513C PHE* 3.9 17.7 - - + +
514C LYS* 1.3 88.3 - - + +
516C LEU* 1.3 58.4 + - - +
517C VAL 6.0 0.2 - - - +
528C VAL* 3.9 29.1 - - + +
530C ARG 4.9 3.6 - - - +
531C ARG* 2.9 30.8 - - + +
532C LYS 4.9 5.8 - - - +
595C VAL 4.9 0.2 - - - +
596C TYR* 4.0 26.5 - - + -
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Residues in contact with LEU 516 (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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514C LYS* 3.6 0.9 + - + +
515C PRO* 1.3 76.6 - - - +
517C VAL* 1.3 68.8 + - + +
527C LEU* 3.2 14.3 - - + +
528C VAL* 2.8 26.3 + - - -
531C ARG* 3.3 35.7 + - - +
587C CYS* 5.2 1.3 - - - -
595C VAL* 2.9 35.8 + - + +
597C LEU* 4.2 36.3 - - + -
727C VAL* 4.5 21.3 - - + -
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Residues in contact with VAL 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C PRO* 6.0 0.2 - - - +
516C LEU* 1.3 93.7 - - + +
518C THR* 1.3 71.3 + - - +
525C LEU* 4.1 29.4 - - + -
526C GLU 3.5 10.5 - - - +
527C LEU* 3.6 19.3 - - + -
528C VAL* 4.3 2.8 - - - +
593C GLY 4.1 4.0 - - - +
594C ASP* 3.3 4.2 - - - +
595C VAL* 2.8 48.6 + - + +
596C TYR* 5.7 1.0 - - - -
725C LEU* 4.2 16.6 - - + -
727C VAL* 4.8 4.0 - - + -
732C SER* 5.3 2.9 - - - -
735C ALA* 4.8 0.2 - - + -
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Residues in contact with THR 518 (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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530A ARG* 5.3 8.7 + - - +
517C VAL* 1.3 76.3 - - - +
519C LEU* 1.3 76.1 + - - +
524C LYS 3.6 0.2 - - - +
525C LEU* 3.5 2.9 - - - -
526C GLU* 3.1 48.7 + - + +
528C VAL* 4.2 19.7 - - + -
593C GLY 4.0 6.5 - - - -
594C ASP* 3.3 16.7 + - - -
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Residues in contact with LEU 519 (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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530A ARG* 5.1 6.6 + - - -
518C THR* 1.3 88.0 + - - +
520C GLN* 1.3 64.4 + - - +
523C ARG* 3.8 9.9 - - + -
524C LYS 3.6 20.0 - - - +
525C LEU* 3.6 17.9 - - + -
592C CYS 3.1 28.9 - - - +
593C GLY* 4.1 2.4 + - - -
594C ASP* 4.1 4.7 + - - +
738C CYS 5.4 0.9 - - - +
739C SER* 3.5 36.8 - - - -
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Residues in contact with GLN 520 (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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530A ARG* 4.8 18.3 + - - +
532A LYS* 3.7 19.1 + - - +
519C LEU* 1.3 80.7 - - - +
521C LYS* 1.3 91.7 + - + +
522C GLU 3.1 4.3 + - - -
523C ARG 3.8 7.8 + - - -
524C LYS* 2.5 32.1 + - + +
526C GLU* 3.1 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