Contacts of the strand formed by residues 537 - 551 (chain C) in PDB entry 3GEF
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 GLU 537 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C THR* 5.6 0.9 - - - +
527C ARG* 2.8 45.6 + - - -
529C ALA* 3.6 9.8 - - + +
530C LEU 3.5 11.7 - - - +
531C ILE* 3.8 16.1 - - + +
535C GLY 3.7 3.8 + - - -
536C GLU* 1.3 81.3 - - - +
538C VAL* 1.3 61.8 + - - +
539C ALA 3.9 9.7 - - - +
540C MET* 3.7 13.3 - - - +
551D GLU* 3.9 7.8 - - - +
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C THR* 3.6 39.8 + - - +
438C GLY* 5.2 3.3 - - - -
440C VAL* 4.6 5.9 - - + +
467C TRP* 3.9 28.0 - - + -
530C LEU* 2.8 31.9 + - + +
532C ASN* 3.8 20.9 - - + +
536C GLU* 3.4 17.0 - - - +
537C GLU* 1.3 73.6 - - - +
539C ALA* 1.3 60.4 + - + +
551D GLU 5.1 0.2 - - - -
552D ASP* 3.4 19.4 - - - +
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Residues in contact with ALA 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C VAL 3.4 23.3 - - - +
441C ALA* 4.2 10.5 - - - -
442C VAL* 4.3 6.5 - - + +
529C ALA* 3.5 2.4 - - - +
530C LEU* 2.9 36.2 + - + +
537C GLU* 3.8 5.2 - - - +
538C VAL* 1.3 82.6 - - + +
540C MET* 1.3 67.2 + - - +
551D GLU* 3.3 15.9 - - - +
552D ASP* 4.8 1.8 - - - -
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Residues in contact with MET 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 4.2 8.8 + - - +
527C ARG* 4.1 17.3 - - + +
528C THR 3.2 13.2 - - - +
529C ALA* 4.2 4.9 - - + -
537C GLU* 3.7 13.9 - - - +
539C ALA* 1.3 78.6 - - - +
541C ARG* 1.3 66.0 + - - +
542C LYS* 3.8 30.3 - - + -
549D VAL* 3.8 28.0 - - + +
550D VAL* 3.4 5.2 - - - +
551D GLU* 2.9 76.0 + - + +
552D ASP* 5.2 0.3 - - - +
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Residues in contact with ARG 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ARG* 5.3 4.0 - - - +
550B VAL* 3.9 3.8 - - - +
552B ASP* 3.0 40.2 + - - -
442C VAL* 2.9 41.8 + - + +
443C GLU* 3.5 18.3 + - - +
444C GLU* 4.6 1.8 - - - +
445C VAL* 3.9 31.4 - - + +
526C LEU 4.2 0.5 - - - +
527C ARG* 3.8 0.5 - - - -
528C THR* 2.9 32.3 + - - -
540C MET* 1.3 75.2 - - - +
542C LYS* 1.3 62.8 + - - +
548D THR* 3.8 28.1 - - + +
549D VAL 3.4 5.2 - - - -
550D VAL* 3.6 19.9 - - + +
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Residues in contact with LYS 542 (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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542B LYS* 5.3 8.9 - - - +
525C SER* 5.9 2.2 - - - -
526C LEU 3.3 12.1 - - - +
527C ARG* 4.1 26.2 - - + +
540C MET* 3.8 22.0 - - + -
541C ARG* 1.3 75.7 - - - +
543C LEU* 1.3 63.8 + - - +
544C VAL* 3.8 27.3 - - + +
547D VAL 3.5 1.6 - - - +
548D THR* 3.2 8.6 - - - +
549D VAL* 2.8 40.7 + - + +
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Residues in contact with LEU 543 (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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447C GLU* 5.7 9.6 - - + +
523C GLY 3.9 21.1 - - - +
524C ASN* 3.7 15.3 - - - +
525C SER* 3.3 6.6 + - - -
526C LEU* 2.8 49.7 + - + +
542C LYS* 1.3 74.3 - - - +
544C VAL* 1.3 61.0 + - - +
546D SER* 3.9 25.8 - - - +
547D VAL 3.6 12.1 - - - +
548D THR* 3.8 16.2 - - + +
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Residues in contact with VAL 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ASN 3.8 1.6 - - - -
525C SER* 5.1 2.0 - - - +
542C LYS* 3.8 35.7 - - + +
543C LEU* 1.3 75.9 - - - +
545C ARG* 1.3 65.0 + - - +
546C SER 3.7 8.1 - - - +
547C VAL* 3.2 33.0 - - + -
546D SER* 3.4 3.9 + - - -
547D VAL* 2.8 42.3 + - + +
549D VAL* 4.6 13.9 - - + -
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Residues in contact with ARG 545 (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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524C ASN* 3.3 33.2 + - + +
525C SER* 4.6 9.6 - - - +
543C LEU 4.2 0.2 + - - -
544C VAL* 1.3 73.2 - - - +
546C SER* 1.3 65.2 + - - +
545D ARG* 3.2 8.8 - - - +
546D SER* 2.9 23.4 + - - +
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Residues in contact with SER 546 (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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544C VAL* 3.7 6.2 - - - +
545C ARG* 1.3 82.1 - - - +
547C VAL* 1.3 69.3 + - - +
447D GLU* 6.0 1.6 - - - -
544D VAL 3.2 10.8 - - - -
545D ARG* 5.0 3.4 - - - -
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Residues in contact with VAL 547 (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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549A VAL* 4.2 15.7 - - + -
544C VAL* 3.2 35.0 - - + -
546C SER* 1.3 74.4 - - - +
548C THR* 1.3 69.0 + - - +
549C VAL* 3.8 23.7 - - + +
542D LYS 3.6 1.2 - - - +
543D LEU* 3.6 2.9 - - - +
544D VAL* 3.0 34.7 + - + +
547D VAL* 4.2 21.3 - - + -
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Residues in contact with THR 548 (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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549A VAL* 3.3 8.0 - - - +
550A VAL* 3.1 58.2 + - + +
552A ASP* 5.7 1.1 - - - -
547C VAL* 1.3 77.5 + - - +
549C VAL* 1.3 63.3 + - - +
550C VAL* 4.3 0.7 - - + -
541D ARG* 3.7 37.3 + - + +
542D LYS 3.3 4.5 - - - +
543D LEU* 4.1 14.6 - - + +
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Residues in contact with VAL 549 (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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547A VAL* 3.7 26.0 - - + -
548A THR 3.3 11.0 - - - +
549A VAL* 5.0 2.2 - - + -
547C VAL* 3.8 19.7 - - + +
548C THR* 1.3 76.0 - - - +
550C VAL* 1.3 74.6 + - - +
551C GLU* 5.9 0.2 - - + -
540D MET* 3.7 21.7 - - + +
541D ARG* 3.3 0.5 - - - +
542D LYS* 2.8 43.6 + - + +
544D VAL* 5.8 4.7 - - + -
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Residues in contact with VAL 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A THR* 2.9 41.3 + - + +
550A VAL* 3.7 31.6 - - + -
541B ARG* 4.1 13.7 - - - +
549C VAL* 1.3 83.9 - - - +
551C GLU* 1.3 67.1 + - - +
552C ASP 4.0 10.5 - - - +
442D VAL 4.9 1.6 - - - +
540D MET* 3.4 15.5 - - - +
541D ARG* 3.8 38.6 - - + +
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Residues in contact with GLU 551 (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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549C VAL* 5.9 0.4 - - + -
550C VAL* 1.3 75.9 - - - +
552C ASP* 1.3 71.4 + - - +
527D ARG* 4.6 5.5 + - - -
537D GLU* 3.9 15.5 - - - +
539D ALA* 3.3 4.5 - - - -
540D MET* 3.0 53.9 + - + +
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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