Contacts of the helix formed by residues 516 - 533 (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 THR 516 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C SER 4.1 0.2 + - - -
515C GLN* 1.3 75.9 - - - +
517C PRO* 1.3 72.6 - - + +
518C PHE* 3.3 31.1 - - + -
519C GLU* 2.9 40.1 + - - +
520C GLN* 2.8 26.7 + - - +
589C SER* 4.0 0.4 - - - +
591C TYR 4.5 0.7 - - - -
592C ALA* 4.0 30.3 - - + +
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Residues in contact with PRO 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C GLN 4.5 0.9 - - - +
516C THR* 1.3 89.6 - - + +
518C PHE* 1.3 63.3 + - + +
520C GLN* 3.3 16.3 + - - +
521C ARG* 3.1 21.7 + - - +
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Residues in contact with PHE 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ASP* 5.6 0.2 - - - -
516C THR* 3.3 30.1 - - + -
517C PRO* 1.3 77.2 - - + +
519C GLU* 1.3 79.2 + - + +
521C ARG* 3.2 8.6 + - - +
522C HIS* 3.1 31.1 + + - -
591C TYR* 3.5 31.4 - + + -
742C TRP* 3.3 70.4 - + + +
745C ILE* 3.8 24.5 - - + -
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Residues in contact with GLU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C SER* 5.3 2.4 - - - -
259C ASP* 5.2 8.0 + - + +
515C GLN* 3.4 22.1 - - + +
516C THR* 2.9 36.4 + - - +
518C PHE* 1.3 88.2 - - + +
520C GLN* 1.3 62.4 + - - +
522C HIS* 3.3 8.9 + - - +
523C ILE* 3.1 26.7 + - + +
589C SER* 2.6 24.1 + - - -
590C LEU* 2.8 38.8 + - + +
591C TYR* 3.7 13.2 - - + -
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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
----------------------------------------------------------
512C TRP* 2.9 74.1 + - + +
513C LEU* 4.2 8.5 + - - +
515C GLN* 3.8 16.0 + - + -
516C THR 2.8 15.4 + - - +
517C PRO* 3.5 16.6 - - - +
518C PHE 3.2 0.2 - - - -
519C GLU* 1.3 77.2 - - - +
521C ARG* 1.3 56.4 + - - +
523C ILE* 3.2 7.0 + - - +
524C VAL* 2.9 31.0 + - - +
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Residues in contact with ARG 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C PRO 3.1 13.4 + - - +
518C PHE* 3.2 11.2 + - - +
520C GLN* 1.3 75.8 - - - +
522C HIS* 1.3 65.8 + - + +
524C VAL* 3.3 11.0 + - - +
525C ASP* 2.8 54.9 + - - +
745C ILE* 3.6 34.2 + - + +
746C PRO* 5.3 3.6 - - - +
749C ASP* 5.8 4.4 + - - -
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ARG* 4.8 2.9 + - - -
257C MET 3.6 7.1 - - - +
259C ASP* 2.6 43.4 + - - +
303C VAL* 4.0 23.8 - - + +
304C TRP 6.4 0.2 - - - -
518C PHE* 3.1 17.6 + + - -
519C GLU* 3.7 8.2 - - - +
520C GLN 3.3 0.2 - - - -
521C ARG* 1.3 84.0 - - + +
523C ILE* 1.3 55.7 + - - +
525C ASP* 3.3 12.9 + - + +
526C GLY* 2.8 28.9 + - - -
692C LEU* 4.8 1.7 - - + +
742C TRP* 4.2 15.7 - + - -
745C ILE* 3.8 23.4 - - + +
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Residues in contact with ILE 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C MET* 4.0 9.9 - - + +
257C MET* 3.6 11.2 - - + +
258C SER* 3.4 32.8 - - - +
511C PHE* 3.8 19.3 - - + -
512C TRP* 3.9 26.0 - - + -
515C GLN* 3.9 17.7 - - + -
519C GLU* 3.1 16.0 + - + +
520C GLN* 3.4 6.7 - - - +
522C HIS* 1.3 71.9 - - - +
524C VAL* 1.4 69.1 + - - +
526C GLY* 3.1 1.2 + - - -
527C PHE* 2.9 48.9 + - + -
554C LEU* 4.2 1.8 - - + -
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Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C TRP* 4.0 18.2 - - + -
520C GLN 2.9 17.6 + - - +
521C ARG* 3.4 14.4 - - - +
523C ILE* 1.4 78.5 - - - +
525C ASP* 1.3 58.4 + - - +
527C PHE* 3.3 2.6 + - - +
528C SER* 2.7 37.3 + - - +
554C LEU* 4.0 11.4 - - + +
557C ALA* 3.8 34.5 - - + -
558C VAL* 4.1 8.5 - - - +
561C ASN* 3.7 22.0 - - - +
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Residues in contact with ASP 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TRP* 6.4 2.0 - - + -
521C ARG* 2.8 49.2 + - - +
522C HIS* 3.6 14.6 - - + +
524C VAL* 1.3 76.5 - - - +
526C GLY* 1.3 57.4 + - - +
528C SER* 3.7 5.6 - - - -
529C PHE* 2.9 32.8 + - - +
561C ASN* 4.4 7.1 + - - -
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Residues in contact with GLY 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ARG* 4.0 21.7 - - - +
257C MET* 3.8 15.0 - - - -
304C TRP* 6.3 1.3 - - - -
522C HIS 2.8 18.9 + - - -
523C ILE 3.1 2.4 + - - -
525C ASP* 1.3 70.4 - - - +
527C PHE* 1.3 65.4 + - - +
529C PHE* 3.9 4.5 - - - +
530C GLU* 3.0 28.6 + - - +
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Residues in contact with PHE 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TRP* 3.8 21.1 - + - -
250C LEU* 5.6 3.4 - - + -
253C VAL* 3.6 33.0 - - + -
254C MET* 3.7 26.7 - - - -
257C MET* 3.9 16.7 - - + -
523C ILE* 2.9 36.6 + - + -
524C VAL 3.7 5.8 - - - +
526C GLY* 1.3 74.2 - - - +
528C SER* 1.3 58.2 + - - +
530C GLU* 3.8 1.6 - - - +
531C LEU* 2.9 44.2 + - + +
543C VAL* 4.6 2.9 - - + -
547C LEU* 3.7 34.3 - - + -
554C LEU* 4.4 10.3 - - + -
558C VAL* 3.9 15.0 - - + -
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Residues in contact with SER 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C VAL 2.7 21.7 + - - -
525C ASP* 3.7 5.8 - - - -
527C PHE* 1.3 76.5 - - - +
529C PHE* 1.3 60.4 + - - +
532C SER* 2.8 29.7 + - - -
558C VAL* 3.8 14.2 - - - -
561C ASN* 2.9 42.7 + - - +
562C LEU* 3.6 10.6 - - - +
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Residues in contact with PHE 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B THR* 5.9 0.7 - - - -
655B ALA* 4.9 8.1 - - + -
656B GLY* 4.4 13.7 - - - -
180C ARG* 6.1 1.3 - - - -
233C GLN* 5.9 2.7 - - - -
235C ALA* 4.5 15.3 - - + -
304C TRP* 3.5 52.3 - + + +
308C GLN* 3.9 14.4 - - - -
525C ASP 2.9 18.6 + - - +
526C GLY* 3.9 4.5 - - - +
528C SER* 1.3 72.9 - - - +
530C GLU* 1.3 79.7 + - + +
532C SER* 3.3 19.3 + - - -
533C LYS* 3.5 41.1 - - + +
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Residues in contact with GLU 530 (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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180C ARG* 3.4 24.2 + - - +
233C GLN* 5.9 0.2 - - - +
234C SER* 2.7 30.8 + - - -
235C ALA* 3.2 34.3 + - + +
240C TRP* 3.2 30.4 + - + +
257C MET* 3.6 12.8 - - - -
304C TRP* 5.7 2.4 - - - -
526C GLY 3.0 21.4 + - - +
527C PHE 4.0 0.7 - - - +
529C PHE* 1.3 85.8 - - + +
531C LEU* 1.3 58.2 - - - +
533C LYS* 2.9 25.1 + - - +
534C VAL* 3.5 7.8 + - - +
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Residues in contact with LEU 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TRP* 3.6 43.5 - - + -
527C PHE* 2.9 27.2 + - + +
530C GLU* 1.3 75.8 - - - +
532C SER* 1.3 59.4 + - - +
534C VAL* 3.1 12.2 + - + +
540C ARG* 3.0 43.1 + - + +
543C VAL* 3.8 29.8 - - + -
544C VAL* 4.7 1.6 - - + -
547C LEU* 5.2 0.2 - - + -
558C VAL* 4.0 13.2 - - + -
562C LEU* 3.6 32.5 - - + -
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Residues in contact with SER 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B MET* 3.2 50.1 - - - +
651B ALA 4.7 3.6 - - - +
652B ALA* 5.6 2.1 - - - +
653B THR* 4.7 10.4 - - - +
656B GLY* 6.3 1.1 - - - -
528C SER 2.8 20.2 + - - -
529C PHE* 3.4 13.1 - - - -
531C LEU* 1.3 75.8 - - - +
533C LYS* 1.3 67.0 + - - +
534C VAL 3.3 1.1 + - - +
540C ARG* 4.1 7.7 + - - +
561C ASN 5.0 0.5 + - - -
562C LEU* 3.6 4.7 - - - +
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Residues in contact with LYS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG 5.3 4.6 + - - -
652B ALA* 5.9 4.7 - - + -
656B GLY* 3.0 35.4 + - - -
233C GLN* 5.8 1.6 + - - -
235C ALA* 3.5 31.2 - - + +
236C HIS* 4.4 2.3 - - - -
237C ASP* 3.9 4.2 - - - +
308C GLN* 5.2 3.8 - - - +
529C PHE* 3.5 44.4 - - + +
530C GLU 2.9 11.1 + - - +
532C SER* 1.3 81.7 - - - +
534C VAL* 1.3 62.5 + - - +
535C VAL* 3.5 10.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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