Contacts of the helix formed by residues 423 - 438 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A THR* 3.6 33.2 - - - +
292A SER* 3.8 14.6 - - - +
293A ARG* 3.3 50.0 - - + +
418B GLU* 2.8 26.6 + - - +
422B ASP* 1.3 75.4 - - - +
424B TRP* 1.3 65.8 + - - +
425B LEU 3.3 2.7 - - - -
426B THR* 3.0 28.4 + - - +
427B HIS* 3.1 29.1 + - + +
523B HIS* 4.2 0.9 - - - -
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Residues in contact with TRP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 3.4 32.1 - - - -
278B THR* 3.0 27.7 + - - -
279B ILE 3.8 17.1 - - - -
280B ILE* 4.1 2.1 - - - +
281B ILE* 3.7 32.8 - - + -
290B PHE* 4.6 6.7 - + - -
294B TYR* 3.7 15.3 - + - -
421B THR* 3.2 27.6 + - - +
422B ASP 3.2 0.4 - - - -
423B LEU* 1.3 76.1 - - - +
425B LEU* 1.3 61.2 + - + +
427B HIS 3.2 1.0 + - - -
428B SER* 3.0 21.5 + - - -
520B ILE* 4.7 3.1 - - + -
521B SER 5.8 0.2 - - - -
522B CYS* 4.0 8.5 - - - -
523B HIS* 3.6 57.0 - + + -
526B LEU* 3.5 19.7 - - + +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.4 20.6 - - + +
280B ILE* 6.1 0.4 - - - -
414B ARG* 3.6 30.3 - - - +
417B LEU* 5.5 2.9 - - + -
418B GLU* 3.2 19.1 + - - +
423B LEU 3.3 0.4 - - - -
424B TRP* 1.3 80.3 - - + +
426B THR* 1.3 59.3 + - - +
428B SER* 3.0 8.3 + - - +
429B LEU* 2.9 52.4 + - + +
461B TYR* 3.5 48.7 - - + +
463B LEU* 4.4 9.2 - - + -
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Residues in contact with THR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A THR* 2.9 27.5 - - + +
293A ARG* 4.3 20.2 - - - +
418B GLU* 2.7 21.7 + - - -
423B LEU* 3.0 16.2 + - + +
425B LEU* 1.3 78.0 - - - +
427B HIS* 1.3 62.5 + - - +
429B LEU* 3.7 9.3 - - - +
430B LYS* 3.0 42.8 + - + +
530B ARG* 6.0 0.2 - - - +
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Residues in contact with HIS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.8 8.1 - - - -
422B ASP 4.4 1.2 + - - -
423B LEU* 3.1 36.5 + - + +
424B TRP 3.5 6.5 - - - +
426B THR* 1.3 81.8 - - + +
428B SER* 1.3 65.5 + - - +
430B LYS* 3.2 4.7 + - - +
431B ALA* 3.1 20.8 + - - +
523B HIS* 3.0 31.6 + + - -
526B LEU* 3.8 14.7 - - + +
527B GLU* 3.2 28.5 + - + -
530B ARG* 3.7 34.0 + - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 4.9 3.0 - - - -
278B THR 4.2 7.2 - - - -
279B ILE* 3.1 47.5 + - - +
424B TRP 3.0 9.4 + - - -
425B LEU* 3.0 17.0 + - - +
427B HIS* 1.3 75.6 - - - +
429B LEU* 1.3 63.6 + - - +
431B ALA* 3.1 6.5 + - - +
432B LEU* 2.9 32.8 + - - +
526B LEU* 3.8 15.8 - - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG* 5.5 4.3 - - - +
425B LEU* 2.9 48.2 + - + +
426B THR* 3.7 7.9 - - - +
428B SER* 1.3 79.0 + - - +
430B LYS* 1.3 50.5 + - + +
432B LEU* 3.2 3.7 + - - +
433B ASN* 2.7 52.2 + - - +
461B TYR 4.8 2.5 - - - +
462B GLY* 4.2 10.3 - - - +
463B LEU* 3.7 25.6 - - + -
466B VAL* 3.9 21.5 - - + -
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ASP* 3.4 25.7 + - - -
503A GLY* 4.4 8.7 - - - -
504A VAL* 4.6 18.1 - - - +
519A ARG* 5.7 7.7 - - - +
426B THR* 3.0 34.9 + - + +
427B HIS 3.2 7.6 + - - +
429B LEU* 1.3 75.2 - - + +
431B ALA* 1.3 61.8 + - - +
433B ASN* 3.6 11.3 + - - +
434B LEU* 3.0 24.8 + - - +
530B ARG* 3.7 32.1 - - - +
534B GLU* 5.5 7.6 - - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 4.1 15.9 - - + -
427B HIS 3.1 8.1 + - - +
428B SER* 3.1 11.1 + - - +
430B LYS* 1.3 78.6 - - - +
432B LEU* 1.3 63.2 + - - +
434B LEU* 3.0 19.5 + - - +
435B ILE* 3.1 14.2 + - - +
526B LEU* 5.0 3.8 - - + -
529B LEU* 5.3 0.7 - - + -
530B ARG* 4.2 19.7 - - + +
533B LEU* 3.8 24.2 - - + +
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TRP* 3.5 23.6 - - + +
279B ILE* 3.8 34.1 - - + -
428B SER* 2.9 18.6 + - - +
429B LEU* 3.5 8.3 - - - +
431B ALA* 1.3 75.9 - - - +
433B ASN* 1.3 63.1 + - - +
435B ILE* 2.9 3.3 + - - -
436B ASN* 2.9 20.3 + - - +
443B ASN* 3.1 41.7 + - + +
463B LEU* 3.9 17.0 - - + -
466B VAL* 4.2 13.5 - - + -
467B PHE* 3.9 19.1 - - + -
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Residues in contact with ASN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A VAL* 3.7 21.5 - - + +
429B LEU* 2.7 42.8 + - - +
430B LYS* 3.9 13.5 - - - +
432B LEU* 1.3 72.5 - - - +
434B LEU* 1.3 57.8 + - - +
436B ASN* 3.3 9.5 + - - +
437B SER* 3.0 29.3 + - - -
466B VAL* 3.5 22.0 - - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A VAL* 4.2 19.3 - - + +
507A GLU* 6.0 1.3 - - - +
508A GLN* 6.0 1.3 - - - +
430B LYS 3.0 14.5 + - - +
431B ALA* 3.1 14.4 - - - +
432B LEU 3.0 0.6 - - - -
433B ASN* 1.3 78.4 - - - +
435B ILE* 1.3 57.4 + - - +
437B SER* 3.0 22.7 + - - +
438B ARG* 3.3 22.2 - - + +
530B ARG* 4.3 2.5 - - + +
533B LEU* 3.6 35.4 - - + +
534B GLU* 3.7 37.7 - - - +
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Residues in contact with ILE 435 (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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271B PHE* 3.3 58.1 - - + -
273B TRP* 3.8 21.8 - - + -
431B ALA 3.1 9.4 + - - +
432B LEU 2.9 3.6 + - - +
434B LEU* 1.3 74.6 - - - +
436B ASN* 1.3 64.8 + - - +
438B ARG* 3.2 19.2 + - - +
441B CYS* 3.0 25.8 - - + +
442B VAL 3.8 10.5 - - - +
443B ASN* 3.3 30.7 - - - +
533B LEU* 4.3 15.9 - - + -
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Residues in contact with ASN 436 (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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432B LEU 2.9 12.0 + - - +
433B ASN* 3.4 15.9 - - - +
435B ILE* 1.3 78.1 - - - +
437B SER* 1.3 63.6 + - - +
438B ARG 3.3 8.7 - - - +
441B CYS 4.5 3.5 - - - +
442B VAL* 6.0 0.7 - - - +
443B ASN* 3.9 7.8 + - - +
465B SER 5.0 2.9 + - - +
466B VAL* 4.1 22.3 - - - +
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Residues in contact with SER 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A VAL* 3.9 22.4 - - - +
505A GLU* 5.5 2.2 - - - -
508A GLN* 3.8 34.2 + - - +
512A LYS* 4.2 4.3 + - - -
433B ASN 3.0 13.8 + - - -
434B LEU* 3.0 22.9 + - - +
436B ASN* 1.3 75.9 - - - +
438B ARG* 1.3 65.7 + - - +
439B PRO* 3.1 10.7 - - - +
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Residues in contact with ARG 438 (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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508A GLN* 5.0 5.2 - - - +
269B ARG* 4.7 1.4 - - - +
271B PHE* 3.9 13.9 - - - -
434B LEU* 3.3 21.5 + - + +
435B ILE* 3.2 19.5 + - - +
436B ASN 3.2 12.1 - - - +
437B SER* 1.3 80.1 + - - +
439B PRO* 1.3 71.1 - - + +
440B ASN 4.7 0.4 - - - +
441B CYS* 3.3 36.7 - - + +
533B LEU* 2.7 35.3 + - - +
536B GLU* 3.3 22.1 - - - +
538B LEU* 2.6 41.9 + - - -
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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