Contacts of the helix formed by residues 480 - 491 (chain B) in PDB entry 2CEA
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 480 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A PRO* 4.9 9.4 - - + +
476B LEU* 3.3 24.2 - - + +
477B THR 3.1 7.7 + - - +
478B ALA 3.0 1.2 - - - -
479B LEU* 1.3 76.0 - - - +
481B GLY* 1.3 59.0 + - - +
482B GLY 3.4 2.0 - - - -
483B ARG* 3.5 12.6 + - + +
484B ALA* 2.9 27.2 + - - +
500B ASP* 4.8 4.7 - - + +
501B ILE* 5.0 10.3 - - + -
504B ALA* 3.9 21.3 - - + -
561B VAL* 3.7 20.2 - - + +
564B CYS 3.9 2.9 - - - -
565B TYR* 3.5 48.9 - - + +
568B ALA* 4.3 2.2 - - + -
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Residues in contact with GLY 481 (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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426B GLY* 3.9 10.8 - - - -
430B VAL* 3.9 25.1 - - - -
477B THR 3.3 2.7 + - - -
478B ALA 2.8 14.4 + - - -
479B LEU 3.3 0.2 - - - -
480B LEU* 1.3 76.5 - - - +
482B GLY* 1.3 55.4 + - - +
484B ALA* 3.1 6.5 + - - +
485B ALA* 2.7 36.4 + - - +
568B ALA* 4.3 0.7 - - - -
572B ILE* 4.5 1.2 - - - +
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Residues in contact with GLY 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B HIS* 3.2 51.3 + - - -
426B GLY* 4.5 0.4 - - - -
427B HIS* 3.9 12.7 - - - +
480B LEU 3.4 0.4 - - - -
481B GLY* 1.3 74.4 - - - +
483B ARG* 1.3 63.8 + - - +
485B ALA* 3.1 3.5 + - - +
486B GLU* 2.9 23.2 + - - +
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Residues in contact with ARG 483 (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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515A LEU* 3.0 15.7 + - - +
516A GLY* 2.6 42.2 + - - -
517A MET* 4.5 0.2 - - - +
523A PRO* 4.3 13.4 - - + +
423B HIS* 3.8 5.1 + - - -
479B LEU 5.2 0.8 + - - +
480B LEU* 3.5 16.3 + - + +
481B GLY 3.2 0.4 - - - -
482B GLY* 1.3 76.3 - - - +
484B ALA* 1.3 56.4 + - - +
486B GLU* 3.2 13.8 + - - +
487B GLU* 2.8 27.9 + - - +
493B VAL* 2.7 48.5 - - - +
494B THR 3.7 9.1 + - - -
497B ALA* 3.7 23.1 - - + +
498B ALA 5.6 0.2 - - - +
500B ASP* 6.3 0.9 - - + +
501B ILE* 4.1 15.1 - - + +
565B TYR* 3.6 24.1 + - + +
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Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU 2.9 17.5 + - - +
481B GLY* 3.4 5.6 - - - +
483B ARG* 1.3 78.2 - - - +
485B ALA* 1.3 61.8 + - - +
487B GLU* 3.2 0.9 + - - +
488B VAL* 3.0 29.3 + - - +
565B TYR* 3.9 11.4 - - + -
568B ALA* 3.7 25.1 - - + -
569B LYS* 3.8 21.3 - - + +
572B ILE* 4.1 6.3 - - + -
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B TYR* 3.3 31.9 - - + +
426B GLY* 3.9 9.0 - - - -
481B GLY 2.7 19.4 + - - +
482B GLY 3.1 3.1 + - - +
484B ALA* 1.3 73.1 - - - +
486B GLU* 1.3 62.8 + - - +
489B VAL* 3.0 30.2 + - - +
572B ILE* 4.1 14.1 - - + +
579B LEU* 4.3 15.5 - - + -
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Residues in contact with GLU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.8 23.4 - - + +
422B TYR* 5.1 0.8 - - - +
423B HIS* 2.8 38.6 + - + +
482B GLY 2.9 10.4 + - - +
483B ARG* 3.2 13.3 - - - +
485B ALA* 1.3 77.2 - - - +
487B GLU* 1.3 64.7 + - - +
490B PHE* 3.0 32.5 + - + +
492B ASP 3.3 15.8 - - - +
493B VAL* 3.8 4.9 - - + +
494B THR* 2.3 49.2 + - - +
496B GLY* 4.7 1.2 - - - -
497B ALA* 4.6 5.7 + - - +
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ARG* 2.8 13.6 + - - +
484B ALA 3.9 2.2 - - - +
486B GLU* 1.3 73.6 - - - +
488B VAL* 1.3 60.2 + - - +
491B GLY* 2.8 42.2 + - - +
492B ASP 3.7 7.9 - - - -
493B VAL* 4.0 10.8 - - + +
565B TYR* 2.4 39.5 + - - +
569B LYS* 3.3 28.4 + - + +
570E GLU* 5.6 1.7 - - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ALA 3.0 20.1 + - - +
487B GLU* 1.3 79.0 - - - +
489B VAL* 1.3 64.3 + - + +
491B GLY* 4.2 1.7 + - - -
569B LYS* 4.1 27.4 - - + -
572B ILE* 3.9 22.7 - - + -
573B ARG* 3.7 39.5 - - + +
576B ARG* 4.3 17.9 + - - +
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 5.6 3.6 - - - +
422B TYR* 3.8 28.3 - - + -
485B ALA 3.0 19.3 + - - +
488B VAL* 1.3 84.4 - - + +
490B PHE* 1.3 91.2 + - + +
576B ARG* 3.6 45.1 + - - +
579B LEU* 3.9 9.4 - - + -
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.3 35.9 - - + -
419B ILE* 4.0 39.7 - - + -
422B TYR* 3.7 38.8 - + + -
486B GLU* 3.0 25.0 + - + +
489B VAL* 1.3 95.3 - - + +
491B GLY* 1.3 58.5 + - - +
492B ASP* 3.1 18.7 + - + +
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Residues in contact with GLY 491 (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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486B GLU 3.6 0.6 + - - -
487B GLU* 2.8 34.4 + - - +
488B VAL 4.2 1.5 + - - -
489B VAL 3.6 1.4 - - - -
490B PHE* 1.3 76.8 - - - +
492B ASP* 1.3 60.5 + - - -
493B VAL* 5.0 0.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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