Contacts of the helix formed by residues 551 - 562 (chain C) in PDB entry 1GGE
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 ASP 551 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509C ARG* 2.6 28.6 + - + +
512C TRP* 3.2 34.2 + - + +
513C LEU* 4.6 2.4 - - - +
547C LEU 3.0 8.3 + - - +
548C ALA 4.3 2.9 + - - -
549C HIS 3.9 0.4 - - - -
550C ILE* 1.3 86.8 - - + +
552C LEU* 1.3 67.0 + - - +
553C THR* 3.0 28.9 + - - -
554C LEU* 3.0 17.4 + - + +
555C ALA* 3.0 18.9 + - - +
575C PRO* 6.0 1.3 - - - -
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Residues in contact with LEU 552 (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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548C ALA* 4.6 8.2 + - + +
551C ASP* 1.3 73.1 + - - +
553C THR* 1.3 62.6 + - - +
555C ALA* 3.3 4.6 + - + +
556C GLN* 2.9 58.1 + - + +
566C LEU* 3.7 13.5 - - + -
570C GLN 4.7 3.8 - - - +
571C LEU* 3.5 46.9 - - + +
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Residues in contact with THR 553 (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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512C TRP* 5.0 9.0 - - + -
551C ASP* 3.0 13.1 + - - -
552C LEU* 1.3 77.6 - - - +
554C LEU* 1.3 67.5 + - - +
556C GLN* 3.5 10.0 + - - +
557C ALA* 3.0 26.0 + - + +
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Residues in contact with LEU 554 (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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254C MET* 3.9 31.2 - - + -
512C TRP* 3.7 42.0 - - + -
523C ILE* 4.2 11.0 - - + -
524C VAL* 4.0 14.4 - - + -
527C PHE* 4.4 4.9 - - + -
547C LEU* 4.0 20.2 - - + -
550C ILE* 4.3 17.3 - - + -
551C ASP* 3.0 16.3 + - + +
553C THR* 1.3 78.2 - - - +
555C ALA* 1.3 64.7 + - - +
557C ALA* 3.4 1.4 + - - +
558C VAL* 3.2 39.8 + - + +
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Residues in contact with ALA 555 (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* 4.2 7.3 - - - +
547C LEU* 3.7 13.0 - - + -
548C ALA* 3.5 42.6 - - + +
551C ASP 3.0 11.3 + - - +
552C LEU* 3.7 4.9 - - - +
554C LEU* 1.3 77.9 - - - +
556C GLN* 1.3 59.2 + - - +
558C VAL* 3.9 1.0 - - - +
559C ALA* 2.9 30.8 + - - +
566C LEU* 4.1 10.5 - - + -
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Residues in contact with GLN 556 (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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552C LEU* 2.9 49.6 + - + +
553C THR* 3.9 8.8 + - - +
555C ALA* 1.3 72.7 - - - +
557C ALA* 1.3 58.5 + - - +
559C ALA* 3.4 4.1 + - - +
560C LYS* 2.8 30.7 + - - +
566C LEU* 3.5 23.3 - - + -
571C LEU* 3.9 11.9 - - + +
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Residues in contact with ALA 557 (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 VAL* 3.8 26.5 - - + -
553C THR* 3.0 19.4 + - + +
554C LEU 3.9 2.5 - - - +
556C GLN* 1.3 76.7 - - - +
558C VAL* 1.3 62.0 + - - +
560C LYS* 3.4 7.8 + - - +
561C ASN* 3.2 26.6 + - - +
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Residues in contact with VAL 558 (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 VAL* 4.1 13.2 - - + +
527C PHE* 3.9 16.8 - - + -
528C SER* 3.8 13.7 - - - +
531C LEU* 4.0 15.7 - - + -
544C VAL* 4.1 4.5 - - + -
547C LEU* 3.8 24.9 - - + -
554C LEU* 3.2 28.8 + - + +
555C ALA 4.0 2.7 - - - +
557C ALA* 1.3 72.1 - - - +
559C ALA* 1.3 67.2 + - - +
561C ASN* 3.1 12.5 + - - +
562C LEU* 3.1 32.8 + - + +
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Residues in contact with ALA 559 (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* 4.0 12.7 - - + +
555C ALA 2.9 19.9 + - - +
556C GLN* 3.6 5.8 - - - +
558C VAL* 1.3 77.3 - - - +
560C LYS* 1.3 56.1 + - - +
562C LEU* 3.1 3.3 + - - -
563C GLY 3.0 8.3 + - - -
564C ILE* 2.7 51.4 + - + +
566C LEU* 3.9 23.1 - - + +
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Residues in contact with LYS 560 (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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636B ARG* 4.1 15.2 - - - +
556C GLN 2.8 18.9 + - - +
557C ALA* 3.7 7.6 - - - +
558C VAL 3.2 0.2 - - - -
559C ALA* 1.3 76.4 - - - +
561C ASN* 1.3 63.8 + - - +
563C GLY* 3.3 12.3 + - - +
564C ILE 4.0 3.6 + - - +
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Residues in contact with ASN 561 (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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636B ARG* 3.7 10.7 - - - +
637B MET* 3.0 25.0 + - - +
653B THR* 5.5 0.5 - - - +
524C VAL* 3.7 13.9 - - - +
525C ASP* 4.4 7.9 + - - -
528C SER* 2.9 39.3 + - - +
532C SER* 5.0 0.7 + - - -
557C ALA 3.2 13.6 + - - +
558C VAL 3.1 5.3 + - - +
560C LYS* 1.3 79.2 - - - +
562C LEU* 1.3 59.8 + - - +
563C GLY 3.4 0.2 - - - -
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Residues in contact with LEU 562 (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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637B MET* 3.8 15.9 - - + +
638B GLY* 3.7 12.0 + - - -
528C SER* 3.6 13.7 - - - +
531C LEU* 3.6 35.9 - - + -
532C SER* 3.6 31.4 - - - +
540C ARG* 4.1 24.2 + - + -
544C VAL* 4.2 2.7 - - + -
558C VAL* 3.1 22.0 + - + +
559C ALA 3.1 5.3 + - - +
561C ASN* 1.3 81.3 - - + +
563C GLY* 1.3 65.1 + - - +
564C ILE* 3.2 21.8 + - + +
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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