Contacts of the helix formed by residues 423 - 438 (chain C) in PDB entry 3GEB
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 423 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLU* 2.9 48.0 + - + +
419C ALA* 5.5 1.6 - - - -
422C ASP* 1.3 78.6 - - - +
424C TRP* 1.3 63.6 + - - +
425C LEU 3.4 2.5 - - - -
426C THR* 3.2 19.7 - - + +
427C HIS* 2.8 34.5 + - + +
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Residues in contact with TRP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLU 3.5 23.1 - - - -
278C THR 3.2 18.6 + - - -
279C ILE 3.3 21.9 + - - -
280C ILE* 4.2 1.7 - - - +
281C ILE* 3.7 24.0 - - + +
290C PHE* 4.0 15.0 - + - -
294C TYR* 4.0 14.4 - - - -
418C GLU* 4.0 0.2 + - - -
421C THR* 3.3 28.2 + - - +
423C LEU* 1.3 73.6 - - - +
425C LEU* 1.3 65.4 + - - +
427C HIS* 2.9 15.6 + - - +
428C SER 3.0 11.1 + - - -
520C ILE* 3.9 14.8 - - + -
521C SER 4.3 5.4 - - - -
522C CYS* 3.8 25.6 - - - -
523C HIS* 3.6 43.1 - + - -
526C LEU* 3.7 11.6 - - + +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE 3.8 17.3 - - - +
280C ILE* 4.0 19.3 - - + -
414C ARG* 3.6 31.9 - - - +
417C LEU* 5.6 1.6 - - + -
418C GLU* 3.2 20.4 + - - +
423C LEU 3.4 0.4 - - - -
424C TRP* 1.3 79.0 - - - +
426C THR* 1.3 53.5 + - - +
428C SER* 3.0 8.9 + - - +
429C LEU* 2.7 51.9 + - + +
461C TYR* 3.6 33.2 - - + +
463C LEU* 4.5 13.5 - - + -
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Residues in contact with THR 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C GLU* 3.0 16.0 + - - -
423C LEU* 3.2 28.5 + - + +
424C TRP 3.2 0.2 - - - -
425C LEU* 1.3 79.9 - - - +
427C HIS* 1.3 62.6 + - + +
429C LEU* 3.7 8.9 - - - +
430C LYS* 3.1 47.9 + - + +
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Residues in contact with HIS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ASP 4.3 1.6 - - - -
423C LEU* 2.8 39.9 + - + +
424C TRP 2.9 9.3 + - - +
426C THR* 1.3 80.5 - - + +
428C SER* 1.3 66.2 + - - +
430C LYS* 3.3 33.5 + - + +
431C ALA* 3.7 4.7 + - - +
523C HIS* 3.8 41.7 - + + +
526C LEU* 4.1 25.2 - - + +
527C GLU* 5.3 11.4 - - + -
530C ARG* 5.6 0.2 - - - +
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Residues in contact with SER 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TRP* 4.6 1.4 - - - -
279C ILE* 2.8 50.7 + - - +
424C TRP 3.0 8.9 + - - -
425C LEU* 3.0 14.9 + - - +
427C HIS* 1.3 76.5 - - - +
429C LEU* 1.3 61.9 + - - +
431C ALA* 3.0 7.3 + - - +
432C LEU* 3.0 24.4 + - - +
526C LEU* 3.9 26.4 - - - +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 6.0 1.8 - - - +
425C LEU* 2.7 46.2 + - + +
426C THR* 3.7 8.1 - - - +
428C SER* 1.3 74.4 + - - +
430C LYS* 1.3 55.4 + - - +
432C LEU* 4.0 7.9 - - + -
433C ASN* 2.7 56.8 + - - +
461C TYR 5.5 1.3 - - - +
462C GLY 4.6 10.1 - - - +
463C LEU* 3.7 25.6 - - + -
466C VAL* 4.4 11.9 - - + -
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Residues in contact with LYS 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C THR* 3.1 46.0 + - + +
427C HIS* 3.4 24.7 + - + +
428C SER 3.2 0.4 - - - -
429C LEU* 1.3 75.6 - - - +
431C ALA* 1.3 59.1 - - - +
433C ASN* 4.2 6.3 - - - +
434C LEU* 3.4 21.0 + - - +
527C GLU* 5.4 2.7 - - - +
530C ARG* 3.9 31.6 - - - +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TRP* 4.0 19.1 - - + -
427C HIS 3.7 4.2 + - - +
428C SER* 3.0 12.1 + - - +
430C LYS* 1.3 78.7 - - - +
432C LEU* 1.3 67.3 + - - +
433C ASN 3.2 0.2 - - - -
434C LEU* 3.0 3.8 + - - +
435C ILE* 3.0 28.5 + - - +
526C LEU* 4.7 5.6 - - + +
529C LEU* 4.4 10.5 - - + -
530C ARG* 4.6 10.3 - - + +
533C LEU* 3.6 18.3 - - + +
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TRP* 3.6 32.5 - - + +
279C ILE* 3.6 31.6 - - + -
428C SER* 3.0 23.3 + - - +
429C LEU* 3.6 9.4 - - + +
431C ALA* 1.3 77.0 - - - +
433C ASN* 1.3 57.6 + - - +
435C ILE 3.4 0.3 + - - -
436C ASN* 3.0 16.5 + - - +
443C ASN* 3.0 30.8 + - - +
463C LEU* 3.8 18.4 - - + -
466C VAL* 4.1 16.8 - - + -
467C PHE* 3.6 27.4 - - + -
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Residues in contact with ASN 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 2.7 46.8 + - - +
430C LYS* 4.2 5.4 - - - +
432C LEU* 1.3 73.0 - - - +
434C LEU* 1.3 58.1 + - - +
436C ASN* 3.9 5.5 - - - +
437C SER* 3.2 26.3 + - - -
465C SER* 5.8 0.2 + - - -
466C VAL* 3.3 21.2 - - - +
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Residues in contact with LEU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LYS 3.4 11.2 + - - +
431C ALA 3.0 8.6 + - - +
433C ASN* 1.3 76.7 - - - +
435C ILE* 1.3 65.6 + - - +
437C SER* 3.1 9.6 + - - +
438C ARG* 3.0 43.4 + - + +
530C ARG* 3.6 23.8 - - + +
533C LEU* 3.2 43.7 - - + +
534C GLU* 3.7 9.0 - - + +
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Residues in contact with ILE 435 (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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271C PHE* 3.5 42.4 - - + -
273C TRP* 3.5 26.9 - - + -
431C ALA 3.0 14.0 + - - +
432C LEU 3.7 3.4 - - - +
434C LEU* 1.3 77.0 - - - +
436C ASN* 1.3 60.0 + - - +
438C ARG* 3.4 3.4 - - - +
441C CYS* 3.0 37.7 - - + +
442C VAL 3.7 10.8 - - - -
443C ASN* 3.1 37.9 - - - +
529C LEU* 5.2 1.1 - - + -
533C LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 436 (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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432C LEU 3.0 15.3 + - - +
433C ASN* 4.0 7.4 - - - +
434C LEU 3.2 0.2 - - - -
435C ILE* 1.3 74.7 - - - +
437C SER* 1.3 66.1 + - - +
438C ARG 3.2 9.4 - - - +
441C CYS 4.4 3.9 - - - +
443C ASN* 3.4 14.4 - - - +
465C SER 4.7 4.7 - - - +
466C VAL* 2.9 40.1 + - + +
468C PRO* 5.0 4.6 - - - +
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Residues in contact with SER 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C ASN 3.2 14.3 + - - -
434C LEU* 3.1 19.1 + - - +
436C ASN* 1.3 75.7 - - - +
438C ARG* 1.3 69.4 + - - +
439C PRO* 3.3 5.7 - - - +
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Residues in contact with ARG 438 (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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537B TYR* 5.0 0.8 + - - -
269C ARG* 5.4 0.2 - - - -
434C LEU* 3.0 32.3 + - + +
435C ILE 3.4 6.4 - - - +
436C ASN 3.2 12.7 - - - +
437C SER* 1.3 81.7 + - - +
439C PRO* 1.3 74.8 - - + +
440C ASN 3.6 0.6 - - - +
441C CYS* 3.4 34.8 + - + +
533C LEU* 2.8 53.4 + - - +
536C GLU* 3.0 47.9 + - - +
537C TYR* 5.7 0.2 - - - +
538C LEU* 3.4 29.7 - - - +
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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