Contacts of the helix formed by residues 535 - 546 (chain B) in PDB entry 2GRN
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 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B MET* 3.7 37.0 - - + +
522B LEU* 4.3 4.5 - - + -
532B ILE* 3.5 36.8 - - + +
533B ALA 4.3 1.5 + - - +
534B ASN* 1.3 74.8 + - - +
536B TYR* 1.3 67.0 + - - +
537B GLY 3.4 1.8 - - - -
538B PRO* 3.3 4.6 - - + +
539B LEU* 2.9 37.8 + - + +
569B ALA* 3.5 33.4 + - + +
570B LEU* 3.7 26.0 - - + -
573B CYS* 4.0 11.7 - - - -
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Residues in contact with TYR 536 (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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480B PHE* 3.5 49.5 - + - -
481B LYS* 4.8 3.6 - - + -
482B ASP* 3.7 20.4 + - - +
534B ASN* 3.2 26.1 + - - +
535B LEU* 1.3 77.5 - - - +
537B GLY* 1.3 67.1 + - - +
539B LEU* 3.7 1.9 - - - +
540B MET* 3.0 44.9 + - + +
573B CYS* 3.6 13.5 - - + -
575B PHE* 5.2 10.4 - + + -
576B ALA* 4.0 16.8 - - + -
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Residues in contact with GLY 537 (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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477B SER* 3.1 24.5 - - - +
478B SER* 4.9 2.4 - - - +
480B PHE* 3.8 16.2 - - - +
534B ASN* 4.8 2.0 + - - +
536B TYR* 1.3 83.6 - - - +
538B PRO* 1.3 63.9 - - - +
540B MET* 3.1 2.9 + - - +
541B ALA* 2.8 30.8 + - - +
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Residues in contact with PRO 538 (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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473B PHE* 4.1 3.7 - - + -
474B LEU* 3.9 18.6 - - + +
477B SER* 3.4 26.9 - - - +
478B SER* 4.8 4.7 - - - +
520B MET* 4.1 17.7 - - + -
532B ILE* 3.5 26.5 - - + -
534B ASN 3.7 6.7 - - - +
535B LEU 3.3 14.1 - - - +
537B GLY* 1.3 89.5 - - - +
539B LEU* 1.3 56.8 + - - +
541B ALA* 3.4 1.6 + - - +
542B LEU* 3.0 36.8 + - - +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B MET* 3.9 19.5 - - + -
535B LEU* 2.9 31.7 + - + +
536B TYR 3.7 3.1 - - - +
538B PRO* 1.3 75.5 - - - +
540B MET* 1.3 59.9 + - - +
542B LEU* 3.4 3.9 + - + -
543B ASN* 2.9 26.9 + - - +
563B VAL* 4.7 8.7 - - + -
570B LEU* 4.1 22.9 - - + -
573B CYS* 3.9 26.9 - - + -
576B ALA* 3.8 20.1 - - + +
577B ARG* 4.1 11.0 - - + +
580B LEU* 3.6 28.8 - - + +
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Residues in contact with MET 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B PHE* 3.7 47.4 - - + -
482B ASP* 5.0 7.0 - - - +
491B GLN* 5.3 1.6 + - - +
536B TYR* 3.0 40.2 + - + +
537B GLY 3.7 3.4 - - - +
539B LEU* 1.3 73.3 - - - +
541B ALA* 1.3 65.5 + - - +
543B ASN* 3.3 17.5 + - - +
544B HIS* 3.2 20.1 + - - +
575B PHE* 4.9 15.7 - - + -
576B ALA* 3.8 28.0 - - + +
579B SER* 5.1 7.0 - - - -
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 3.5 19.7 - - + -
477B SER* 3.5 22.9 - - - -
480B PHE* 5.0 3.1 - - + -
490B VAL* 4.8 7.2 - - + -
491B GLN* 6.1 2.7 - - - +
494B VAL* 4.1 15.6 - - + +
537B GLY 2.8 17.2 + - - +
538B PRO 3.7 0.7 - - - +
540B MET* 1.3 76.3 - - - +
542B LEU* 1.3 58.1 + - - +
544B HIS* 3.2 8.9 + - - +
545B MET* 2.9 27.4 + - - +
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Residues in contact with LEU 542 (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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473B PHE* 3.9 11.9 - - + -
512B PHE* 5.8 0.2 - - + -
516B LEU* 3.9 19.7 - - + -
520B MET* 4.2 29.8 - - + -
538B PRO 3.0 22.0 + - - +
539B LEU* 3.7 4.5 - - + +
540B MET 3.3 0.2 - - - -
541B ALA* 1.3 75.5 - - - +
543B ASN* 1.3 66.4 + - - +
545B MET* 3.4 31.4 - - + -
546B VAL* 3.0 29.3 + - - +
559B LEU* 4.0 25.1 - - + -
563B VAL* 5.6 0.4 - - + -
580B LEU* 4.1 24.5 - - + -
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Residues in contact with ASN 543 (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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539B LEU 2.9 15.3 + - - +
540B MET* 3.3 23.9 + - - +
541B ALA 3.2 0.4 - - - -
542B LEU* 1.3 75.4 - - - +
544B HIS* 1.3 63.0 + - - +
546B VAL* 3.3 12.7 - - - +
547B GLN* 2.9 30.3 + - - +
576B ALA 5.7 0.2 - - - +
579B SER* 3.2 21.6 + - - +
580B LEU* 3.4 16.2 - - + +
583B THR* 2.5 30.4 + - - +
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Residues in contact with HIS 544 (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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491B GLN* 3.5 58.3 + - + +
492B ASP* 5.8 0.2 + - - -
494B VAL* 5.2 3.4 - - + -
495B ASP* 2.7 43.6 + - - -
540B MET 3.2 6.3 + - - +
541B ALA* 3.2 10.2 + - - +
542B LEU 3.1 0.2 - - - -
543B ASN* 1.3 79.6 - - - +
545B MET* 1.3 65.6 + - - +
547B GLN* 3.1 16.9 + - - +
548B GLN* 3.1 39.7 + - - -
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Residues in contact with MET 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 4.5 6.7 - - - -
494B VAL* 4.3 5.8 - - + -
498B MET* 3.9 26.5 - - - +
502B PHE* 4.2 11.0 - - + -
512B PHE* 4.8 10.5 - - + -
513B LEU* 6.6 0.7 - - + -
516B LEU* 5.5 0.2 - - + -
541B ALA 2.9 17.6 + - - +
542B LEU* 3.4 32.8 - - + +
544B HIS* 1.3 78.0 - - - +
546B VAL* 1.3 60.8 + - + +
548B GLN* 3.0 25.7 + - - +
550B TYR* 3.5 31.4 - - + +
551B PHE* 3.5 37.1 - - + +
555B LEU* 6.1 0.2 - - + -
559B LEU* 4.9 1.8 - - + -
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU 3.0 14.3 + - - +
543B ASN* 3.3 21.3 - - - +
545B MET* 1.3 75.8 - - + +
547B GLN* 1.3 57.3 + - - +
548B GLN 3.3 2.9 + - - +
551B PHE* 3.7 46.1 - - + -
559B LEU* 4.1 13.7 - - + -
580B LEU* 4.4 6.3 - - + -
583B THR* 3.4 23.3 - - + -
584B LEU* 4.0 22.0 - - + -
587B VAL* 4.3 15.6 - - + +
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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