Contacts of the helix formed by residues 423 - 438 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C THR* 3.6 29.8 - - - +
292C SER* 3.7 17.0 - - - +
293C ARG* 3.7 43.7 - - + +
418D GLU* 2.9 41.8 + - - +
421D THR 3.4 0.2 - - - -
422D ASP* 1.3 76.1 - - - +
424D TRP* 1.3 64.7 + - - +
425D LEU 3.4 2.0 - - - -
426D THR* 3.3 14.7 + - + +
427D HIS* 2.9 39.1 + - + +
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Residues in contact with TRP 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D GLU* 3.8 21.8 - - + -
278D THR* 2.8 30.5 + - - -
279D ILE 3.3 19.8 + - - -
280D ILE* 4.1 3.0 - - - +
281D ILE* 3.7 31.0 - - + -
290D PHE* 4.8 5.2 - + - -
293D ARG* 6.1 0.4 - - - -
294D TYR* 3.6 17.5 - + - -
418D GLU* 4.0 0.2 + - - -
421D THR* 3.5 26.0 + - - +
422D ASP 3.4 3.0 - - - -
423D LEU* 1.3 75.9 - - - +
425D LEU* 1.3 59.6 + - - +
427D HIS* 2.9 6.1 + - - +
428D SER 2.9 23.7 + - - -
520D ILE* 4.6 5.2 - - + -
522D CYS* 3.9 8.1 - - - -
523D HIS* 3.6 57.4 - + + -
526D LEU* 3.3 18.4 - - + +
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ILE 4.0 10.3 - - - +
280D ILE* 4.2 17.3 - - + -
414D ARG* 3.5 31.0 - - - +
417D LEU* 6.0 2.9 - - + -
418D GLU* 3.3 17.4 + - - +
423D LEU 3.4 0.2 - - - -
424D TRP* 1.3 76.4 - - + +
426D THR* 1.3 59.5 + - - +
428D SER* 3.0 12.8 + - - +
429D LEU* 2.8 53.3 + - + +
461D TYR* 3.3 41.3 - - + +
463D LEU* 4.4 7.9 - - + -
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Residues in contact with THR 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C THR* 3.0 28.4 - - + +
293C ARG* 4.6 15.9 - - - +
418D GLU* 2.7 19.9 + - - -
423D LEU* 3.3 23.5 + - + +
424D TRP 3.2 0.4 - - - -
425D LEU* 1.3 79.0 - - - +
427D HIS* 1.3 66.3 + - - +
429D LEU* 3.7 10.0 - - - +
430D LYS* 3.0 38.3 + - + +
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Residues in contact with HIS 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ARG* 5.7 3.8 - - - -
422D ASP 3.8 9.1 + - - -
423D LEU* 2.9 34.2 + - + +
424D TRP 2.9 6.3 + - - +
426D THR* 1.3 81.4 - - + +
428D SER* 1.3 63.7 + - - +
430D LYS* 3.2 10.0 + - - +
431D ALA* 3.2 18.4 + - - +
523D HIS* 2.8 34.3 - + + -
526D LEU* 4.1 12.0 - - + +
527D GLU* 3.8 13.4 + - - -
530D ARG* 3.2 42.5 + - - +
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TRP* 4.9 3.3 - - - -
278D THR 4.5 0.7 - - - -
279D ILE* 2.7 52.2 + - - +
424D TRP 2.9 6.8 + - - -
425D LEU* 3.0 18.9 + - - +
427D HIS* 1.3 74.6 - - - +
429D LEU* 1.3 50.3 + - - +
431D ALA* 3.1 6.1 + - - +
432D LEU* 2.8 39.9 + - - +
526D LEU* 3.9 19.9 - - - +
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ARG* 5.5 2.7 - - - +
425D LEU* 2.8 49.1 + - + +
426D THR* 3.7 8.3 - - - +
428D SER* 1.3 74.9 + - - +
430D LYS* 1.3 59.3 + - + +
432D LEU* 3.7 3.5 - - + +
433D ASN* 2.8 45.7 + - - +
461D TYR 4.7 4.0 - - - +
462D GLY* 4.1 9.6 - - - +
463D LEU* 3.9 18.4 - - + -
466D VAL* 3.7 29.6 - - + -
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Residues in contact with LYS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ASP* 3.7 24.7 + - - +
503C GLY* 5.0 4.2 - - - -
504C VAL* 4.8 15.7 - - + +
519C ARG* 6.3 1.0 - - - +
426D THR* 3.0 33.8 + - + +
427D HIS* 3.2 9.8 + - - +
429D LEU* 1.3 76.6 - - + +
431D ALA* 1.3 64.4 + - - +
433D ASN* 3.9 5.5 - - - +
434D LEU* 3.1 26.3 + - - +
530D ARG* 3.6 20.9 - - + +
534D GLU* 5.3 8.5 - - - +
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TRP* 4.0 13.7 - - + -
427D HIS 3.2 8.1 + - - +
428D SER* 3.1 12.7 + - - +
430D LYS* 1.3 80.9 - - - +
432D LEU* 1.3 60.3 + - - +
434D LEU* 3.4 6.7 + - - +
435D ILE* 3.3 27.9 + - - +
526D LEU* 5.0 4.3 - - + -
529D LEU* 5.2 1.3 - - + -
530D ARG* 4.3 18.8 - - + +
533D LEU* 3.8 23.3 - - + +
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Residues in contact with LEU 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TRP* 3.4 40.2 - - + +
279D ILE* 4.0 15.7 - - + -
428D SER 2.8 28.7 + - - +
429D LEU* 3.7 9.2 - - + +
431D ALA* 1.3 73.0 - - - +
433D ASN* 1.3 58.3 + - - +
434D LEU 3.1 0.2 + - - -
435D ILE 3.2 1.7 + - - -
436D ASN* 3.0 15.4 + - - +
443D ASN* 3.0 31.5 + - - +
463D LEU* 3.7 30.1 - - + -
466D VAL* 3.6 16.6 - - + -
467D PHE* 3.9 17.7 - - + -
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Residues in contact with ASN 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C VAL* 4.0 17.3 - - + +
429D LEU* 2.8 41.9 + - - +
430D LYS* 4.0 5.6 - - - +
432D LEU* 1.3 72.1 - - - +
434D LEU* 1.3 59.7 + - - +
436D ASN* 3.5 13.3 + - - +
437D SER* 3.3 23.7 + - - -
465D SER* 5.5 1.7 + - - -
466D VAL* 3.6 21.0 - - - +
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Residues in contact with LEU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C VAL* 3.8 26.5 - - + -
430D LYS 3.1 18.8 + - - +
431D ALA* 3.4 8.3 - - - +
432D LEU 3.1 0.2 - - - -
433D ASN* 1.3 75.6 - - - +
435D ILE* 1.3 64.4 + - + +
437D SER* 2.8 18.2 + - - +
438D ARG* 3.3 22.6 + - + +
530D ARG* 4.3 3.4 - - + +
533D LEU* 3.8 18.8 - - + +
534D GLU* 3.8 50.5 - - + +
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PHE* 3.4 45.1 - - + -
273D TRP* 3.5 23.6 - - + -
431D ALA 3.5 11.4 - - - +
432D LEU 3.2 0.8 + - - +
434D LEU* 1.3 73.3 - - + +
436D ASN* 1.3 68.6 + - - +
438D ARG* 3.3 20.2 + - - +
441D CYS* 3.2 19.2 - - + +
442D VAL 3.9 7.4 - - - +
443D ASN* 3.2 34.5 - - - +
533D LEU* 3.8 22.4 - - + -
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Residues in contact with ASN 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D LEU 3.0 13.5 + - - +
433D ASN* 3.5 19.3 + - - +
435D ILE* 1.3 82.0 - - - +
437D SER* 1.3 63.9 + - - +
438D ARG 3.0 11.8 + - - +
441D CYS 4.2 4.7 - - - +
442D VAL* 6.0 1.1 - - - +
443D ASN* 3.9 5.5 + - - +
465D SER 5.6 0.5 - - - +
466D VAL* 4.4 22.7 - - + +
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Residues in contact with SER 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C VAL* 3.0 30.7 - - - +
505C GLU* 5.3 2.9 - - - -
508C GLN* 3.6 35.0 + - - +
512C LYS* 4.7 1.0 + - - -
433D ASN 3.3 6.9 + - - -
434D LEU* 2.8 21.3 + - - +
436D ASN* 1.3 79.9 - - - +
438D ARG* 1.3 63.2 + - - +
439D PRO* 3.3 4.3 - - - +
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Residues in contact with ARG 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C GLN* 5.0 4.7 - - - +
269D ARG* 4.8 1.8 - - - +
271D PHE* 3.9 15.2 - - - -
434D LEU* 3.3 21.3 + - + +
435D ILE* 3.4 15.3 - - - +
436D ASN 3.0 12.3 + - - +
437D SER* 1.3 80.0 + - - +
439D PRO* 1.3 75.2 - - + +
440D ASN 3.3 1.1 + - - +
441D CYS* 3.5 36.4 + - + +
533D LEU* 2.8 34.3 + - - +
536D GLU* 3.6 17.3 - - - +
538D LEU* 2.5 42.0 + - - -
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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
------------------------------------------------------------
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