Contacts of the helix formed by residues 427 - 447 (chain B) in PDB entry 4CCN
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 427 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A MET* 3.9 6.6 - - - +
450A PHE 3.6 9.1 + - - -
451A ARG* 3.1 27.6 - - - +
452A ARG 3.2 11.4 - - - -
454A LEU* 3.5 14.6 - - - +
371B LEU* 4.6 9.2 - - + -
401B ARG* 3.6 20.4 - - - +
425B ARG* 4.8 2.9 - - - +
426B ASN* 1.3 82.8 - - - +
428B TRP* 1.3 64.8 + - - +
429B GLY 3.4 9.0 + - - -
430B ASP* 2.7 32.9 + - - +
431B PHE 3.3 8.1 + - - -
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU 4.2 11.0 - - - +
450A PHE* 3.9 2.9 + - - +
452A ARG* 3.1 31.9 + - + +
453A GLY 3.6 14.3 + - - -
454A LEU* 3.6 14.3 - - + +
455A PRO* 4.0 19.2 - - + +
477A PHE* 3.4 41.3 - + - -
480A LYS* 3.5 44.9 - - + +
481A VAL* 3.5 27.8 - - + -
484A LEU* 3.7 31.9 - - + -
427B THR* 1.3 71.8 - - - +
429B GLY* 1.3 59.2 + - - +
431B PHE* 3.2 8.2 + + - +
432B LEU* 2.8 35.1 + - + +
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Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 3.7 8.9 - - - +
444A MET* 3.6 24.9 - - - -
450A PHE* 2.9 25.5 + - - -
427B THR* 3.2 1.2 + - - -
428B TRP* 1.3 78.4 - - - +
430B ASP* 1.3 50.6 + - - +
432B LEU* 3.1 4.0 + - - +
433B GLU* 2.7 36.0 + - - +
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Residues in contact with ASP 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A MET* 3.7 8.4 - - - +
371B LEU* 5.4 0.5 - - - +
425B ARG* 2.9 61.5 + - - +
427B THR* 2.7 27.7 + - - +
429B GLY* 1.3 74.4 - - - +
431B PHE* 1.3 59.2 + - - +
433B GLU* 3.3 30.5 - - - +
434B ALA* 3.5 10.2 + - - +
501B ARG* 4.0 16.7 + - - +
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 4.1 20.2 - - + -
458A PHE* 4.3 5.2 - + - -
477A PHE* 3.7 24.0 - + - -
481A VAL* 4.2 11.2 - - + -
427B THR 3.3 9.2 + - - +
428B TRP* 3.2 11.2 + + - +
429B GLY 3.1 0.4 - - - -
430B ASP* 1.3 77.2 - - - +
432B LEU* 1.3 64.8 + - + +
434B ALA* 3.1 5.9 + - - +
435B ILE* 3.0 45.8 + - + +
494B VAL* 3.4 41.5 - - + -
497B VAL* 3.7 18.3 - - + +
498B ALA* 4.1 13.0 - - + -
501B ARG* 3.5 28.2 - - - +
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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
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440A VAL* 4.1 9.4 - - + -
450A PHE* 3.6 36.3 - - + -
481A VAL* 4.3 24.5 - - + -
484A LEU* 3.8 23.6 - - + -
485A VAL* 4.4 14.1 - - + +
488A LEU* 4.3 14.6 - - + -
428B TRP* 2.8 19.8 + - + +
429B GLY 3.5 4.3 - - - +
431B PHE* 1.3 81.5 - - + +
433B GLU* 1.3 65.8 + - - +
435B ILE* 4.0 6.3 - - + -
436B LEU* 3.0 40.9 + - + +
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Residues in contact with GLU 433 (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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437A PRO* 5.1 3.2 - - + +
440A VAL* 4.3 22.9 - - + +
441A GLN* 5.1 8.1 - - - +
444A MET* 4.2 16.0 - - - +
425B ARG* 5.1 2.6 + - - -
429B GLY 2.7 12.2 + - - +
430B ASP* 3.3 30.6 - - - +
431B PHE 3.1 0.2 - - - -
432B LEU* 1.3 77.2 - - - +
434B ALA* 1.3 56.3 + - - +
436B LEU* 5.1 0.4 - - - -
437B PRO* 3.3 22.7 - - - +
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Residues in contact with ALA 434 (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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430B ASP 3.5 7.5 + - - +
431B PHE 3.1 8.3 + - - +
432B LEU 3.1 0.2 - - - -
433B GLU* 1.3 80.7 - - - +
435B ILE* 1.3 66.5 + - - +
437B PRO* 3.4 9.1 - - - +
438B LEU* 3.8 17.3 - - + +
497B VAL* 3.7 23.6 - - + -
501B ARG* 6.1 2.0 - - + +
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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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481A VAL* 5.1 5.6 - - + -
485A VAL* 5.3 3.8 - - + -
431B PHE* 3.0 37.5 + - + +
432B LEU* 3.1 13.2 + - + +
434B ALA* 1.3 74.7 - - - +
436B LEU* 1.3 77.4 + - + +
438B LEU* 2.9 9.4 + - - +
439B ALA* 2.9 20.7 + - + -
492B ALA* 3.4 28.0 - - + -
493B PRO* 3.9 3.8 - - + +
494B VAL* 3.6 33.7 - - + +
497B VAL* 3.4 25.8 - - + -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 3.8 50.3 - - + +
437A PRO* 5.4 0.7 - - + -
440A VAL* 4.0 14.4 - - + -
485A VAL* 4.4 24.7 - - + -
488A LEU* 3.4 34.8 - - + -
432B LEU* 3.0 21.4 + - + +
433B GLU* 5.1 0.4 - - - -
435B ILE* 1.3 75.1 - - + +
437B PRO* 1.3 71.5 - - + +
439B ALA* 2.9 7.5 + - + +
440B VAL* 2.8 27.6 + - - +
488B LEU* 4.9 3.1 - - + -
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Residues in contact with PRO 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 5.3 0.4 - - + +
436A LEU* 5.6 0.4 - - + -
437A PRO* 5.3 14.6 - - + -
433B GLU 3.3 23.1 - - - +
434B ALA* 3.4 10.5 - - - +
436B LEU* 1.3 94.2 - - + +
438B LEU* 1.3 62.7 + - + +
440B VAL* 3.0 26.9 - - + +
441B GLN* 3.2 11.9 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ALA* 3.8 16.2 - - + +
435B ILE 2.9 4.0 + - - +
437B PRO* 1.3 77.1 - - + +
439B ALA* 1.3 60.6 + - - +
441B GLN* 3.3 20.8 + - - +
442B ALA* 2.9 30.3 + - - +
493B PRO* 3.5 29.7 - - + +
496B ALA* 5.2 7.2 - - + -
497B VAL* 4.1 13.5 - - + -
500B GLN* 6.5 0.9 - - + -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 2.9 15.9 + - + +
436B LEU* 3.4 13.9 - - + +
438B LEU* 1.3 77.2 - - - +
440B VAL* 1.3 57.7 + - - +
442B ALA* 3.3 2.3 + - - +
443B ALA* 2.9 30.0 + - - +
488B LEU* 4.1 23.5 - - + +
491B PHE* 3.8 14.5 - - - +
492B ALA* 3.9 21.8 - - - -
493B PRO* 4.0 0.8 - - - +
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Residues in contact with VAL 440 (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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429A GLY* 3.8 22.7 - - - +
432A LEU* 3.8 26.0 - - + -
433A GLU* 4.2 26.7 - - + +
436A LEU* 4.3 12.3 - - + -
436B LEU 2.8 16.5 + - - +
437B PRO* 3.0 26.9 - - + +
439B ALA* 1.3 71.3 - - - +
441B GLN* 1.3 67.1 + - - +
443B ALA* 3.9 0.7 - - - +
444B MET* 3.1 38.3 + - + +
450B PHE* 5.1 1.6 - - + -
488B LEU* 3.9 10.0 - - + +
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Residues in contact with GLN 441 (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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433A GLU* 4.9 9.6 - - - +
437B PRO 3.2 11.5 + - - +
438B LEU* 3.6 26.9 - - - +
439B ALA 3.2 0.2 - - - -
440B VAL* 1.3 84.6 - - + +
442B ALA* 1.3 63.1 + - - +
444B MET* 3.4 7.2 + - - +
445B GLU* 3.1 49.2 + - + +
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Residues in contact with ALA 442 (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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438B LEU 2.9 17.7 + - - +
439B ALA 3.6 3.8 - - - +
441B GLN* 1.3 78.2 - - - +
443B ALA* 1.3 58.0 + - - +
445B GLU* 3.1 10.9 + - - +
446B GLU* 2.9 52.7 + - - +
491B PHE* 3.9 20.2 - - + +
493B PRO* 5.8 1.1 - - + -
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Residues in contact with ALA 443 (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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439B ALA 2.9 18.2 + - - +
440B VAL 3.9 4.0 - - - +
441B GLN 3.4 0.2 - - - -
442B ALA* 1.3 76.6 - - - +
444B MET* 1.3 57.1 + - - +
447B ASN* 2.9 35.2 + - - +
450B PHE* 3.6 30.3 - - + -
488B LEU* 4.2 5.2 - - + -
491B PHE* 3.6 31.3 - - + +
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Residues in contact with MET 444 (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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371A LEU* 3.6 34.1 - - + -
425A ARG* 4.4 4.0 - - - +
427A THR* 3.1 27.8 - - - +
429A GLY* 3.4 33.9 - - - +
430A ASP* 3.7 10.8 - - - +
433A GLU* 4.3 16.8 - - - +
440B VAL* 3.1 25.1 + - + +
441B GLN* 3.7 6.3 - - - +
442B ALA 3.2 0.2 - - - -
443B ALA* 1.3 76.3 - - - +
445B GLU* 1.3 54.9 + - - +
450B PHE* 3.8 18.4 - - + +
451B ARG* 2.7 42.2 + - + +
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Residues in contact with GLU 445 (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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366A THR* 3.9 21.1 - - - +
371A LEU* 5.0 10.5 - - + -
441B GLN* 3.1 42.2 + - + +
442B ALA* 3.1 12.9 + - - +
444B MET* 1.3 79.0 - - - +
446B GLU* 1.3 63.5 + - + +
451B ARG* 3.8 7.7 + - - +
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 5.2 7.1 - - + +
442B ALA* 2.9 36.4 + - - +
445B GLU* 1.3 87.7 - - + +
447B ASN* 1.3 61.1 + - - +
451B ARG* 4.3 2.5 - - - -
491B PHE* 3.7 26.7 - - + -
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Residues in contact with ASN 447 (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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443B ALA 2.9 22.1 + - - +
444B MET 3.7 1.2 - - - +
446B GLU* 1.3 80.3 + - - +
448B VAL* 1.3 67.2 + - - +
449B GLU* 3.1 32.2 + - - +
450B PHE* 3.2 21.1 + - + +
451B ARG* 3.4 10.8 + - - +
487B ARG* 3.5 19.9 + - - +
491B PHE* 3.9 23.1 - - + -
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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