Contacts of the helix formed by residues 497 - 514 (chain C) 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 ALA 497 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C HIS* 4.1 16.6 - - + +
483C ARG* 3.8 46.2 - - + +
486C GLU* 4.6 3.5 + - - +
494C THR 3.9 2.9 + - - +
495C SER 2.9 1.6 + - - -
496C GLY* 1.3 75.3 - - - +
498C ALA* 1.3 64.9 + - - +
499C ASN 3.3 2.7 - - - -
500C ASP* 3.1 12.4 + - + +
501C ILE* 3.0 25.2 + - + +
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Residues in contact with ALA 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLN* 4.3 21.4 - - + +
515B LEU* 4.4 15.0 - - + +
495C SER* 2.9 15.8 + - - +
496C GLY 3.3 1.4 + - - -
497C ALA* 1.3 77.9 - - - +
499C ASN* 1.3 58.8 + - - +
501C ILE* 3.1 6.8 + - - +
502C GLU* 2.9 28.7 + - - +
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Residues in contact with ASN 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C TYR* 6.1 0.5 - - - -
458C HIS* 3.1 22.6 - - + +
496C GLY 3.9 15.4 + - - +
498C ALA* 1.3 77.2 - - - +
500C ASP* 1.3 97.4 + - - +
502C GLU* 3.4 13.6 + - - +
503C ARG* 2.9 23.6 + - - +
1607C ZN 4.4 3.0 - - - -
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Residues in contact with ASP 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C HIS* 3.2 9.7 + - - -
427C HIS* 2.9 9.9 + - - -
458C HIS* 2.5 35.8 + - - -
479C LEU* 3.5 26.0 - - + +
480C LEU* 5.1 4.3 - - + -
483C ARG* 5.3 0.8 + - + -
497C ALA* 3.1 11.2 + - + +
499C ASN* 1.3 88.3 + - - +
501C ILE* 1.3 59.0 + - + +
503C ARG* 3.3 2.1 + - - +
504C ALA* 2.8 31.9 + - - +
1607C ZN 2.0 37.5 - - - -
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Residues in contact with ILE 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLN 4.0 8.3 - - - +
515B LEU* 3.6 33.0 - - - +
516B GLY* 3.9 4.5 - - - +
523B PRO* 3.8 16.8 - - + +
524B LEU 3.5 7.6 - - - -
525B ALA* 3.3 30.7 - - + +
480C LEU* 4.8 6.5 - - + -
483C ARG* 3.7 28.5 - - - +
497C ALA* 3.0 18.7 + - + +
498C ALA 3.4 6.7 - - - +
500C ASP* 1.3 77.4 - - + +
502C GLU* 1.3 54.8 + - - +
504C ALA* 3.3 6.6 + - - +
505C THR* 2.7 37.4 + - - -
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Residues in contact with GLU 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ALA* 3.8 19.3 - - + -
528B LYS* 4.9 21.0 + - - +
498C ALA 2.9 15.8 + - - +
499C ASN* 3.8 12.6 - - - +
501C ILE* 1.3 77.2 - - - +
503C ARG* 1.3 62.5 + - - +
505C THR* 3.5 1.7 + - - -
506C GLU* 3.2 38.8 + - + +
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Residues in contact with ARG 503 (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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310C ASP* 3.0 30.9 + - - +
311C ILE* 6.1 0.4 - - - +
457C LEU 5.5 0.2 - - - +
458C HIS* 2.7 60.4 + - + +
459C LEU 4.7 4.8 + - - -
460C PRO* 4.7 4.8 - - - +
475C LYS* 5.8 5.8 - - - +
479C LEU* 3.4 21.1 - - + -
499C ASN 2.9 18.1 + - - +
500C ASP 3.8 0.4 - - - +
501C ILE 3.2 0.2 - - - -
502C GLU* 1.3 75.4 - - - +
504C ALA* 1.3 70.2 + - - +
506C GLU* 3.3 23.4 + - - +
507C ILE* 3.2 35.7 + - + +
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Residues in contact with ALA 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LEU* 3.3 32.1 - - + +
479C LEU* 4.0 9.1 - - + +
480C LEU* 4.2 21.8 - - + -
500C ASP 2.8 19.1 + - - +
501C ILE* 3.6 4.7 - - - +
503C ARG* 1.3 77.4 - - - +
505C THR* 1.3 63.2 + - - +
507C ILE* 3.1 5.6 + - - +
508C ALA* 3.0 19.2 + - - +
561C VAL* 4.6 7.6 - - + -
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Residues in contact with THR 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B PRO 4.5 1.2 + - - -
524B LEU* 3.7 14.5 - - + +
525B ALA* 3.0 43.9 + - + +
526B TRP* 6.3 1.6 - - + -
501C ILE 2.7 21.0 + - - -
502C GLU 3.9 3.8 - - - -
504C ALA* 1.3 74.1 - - - +
506C GLU* 1.3 66.0 + - - +
507C ILE 3.2 0.2 + - - -
508C ALA* 3.2 6.9 + - - +
509C ARG* 2.9 32.6 + - + +
557C VAL* 4.4 15.5 - - + -
561C VAL* 4.6 4.3 - - - +
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Residues in contact with GLU 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C GLU* 3.2 31.8 + - + +
503C ARG* 3.3 33.5 + - - +
505C THR* 1.3 77.3 - - - +
507C ILE* 1.3 62.5 + - + +
509C ARG* 3.9 7.8 - - - +
510C ASN* 3.1 24.9 + - - +
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Residues in contact with ILE 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU* 4.2 23.1 - - + +
475C LYS* 4.1 28.0 - - + +
476C LEU* 3.9 21.3 - - + -
479C LEU* 4.0 21.5 - - + -
503C ARG* 3.2 27.1 + - + +
504C ALA* 3.1 9.2 + - - +
506C GLU* 1.3 75.4 - - + +
508C ALA* 1.3 62.8 + - - +
510C ASN* 3.3 7.3 + - + +
511C MET* 2.9 42.0 + - + +
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Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C LEU* 4.2 6.2 - - + +
504C ALA 3.0 6.2 + - - +
505C THR 3.5 8.3 - - - +
507C ILE* 1.3 75.5 - - - +
509C ARG* 1.3 65.5 + - - +
511C MET* 3.0 22.2 + - - +
512C VAL* 3.1 17.2 + - - +
557C VAL* 3.6 28.0 - - + +
560C ILE* 4.6 7.0 - - + -
561C VAL* 3.7 21.8 - - + -
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Residues in contact with ARG 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B TRP* 5.6 3.4 - - - -
544B ASN* 2.9 53.7 + - - +
545B TYR* 5.3 0.4 - - - +
505C THR* 2.9 25.8 + - + +
506C GLU* 3.9 7.2 - - - +
508C ALA* 1.3 75.8 - - - +
510C ASN* 1.3 53.3 + - - +
512C VAL* 3.3 0.8 + - - -
513C CYS* 2.7 50.5 + - - +
514C GLN* 4.7 1.6 - - - +
545C TYR* 3.5 22.4 + - - -
553C ILE* 3.9 19.4 - - - +
554C ASP* 3.5 16.8 + - - -
557C VAL* 3.9 23.2 - - + +
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Residues in contact with ASN 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C GLU 3.1 15.8 + - - +
507C ILE* 3.5 8.1 - - - +
509C ARG* 1.3 79.8 - - - +
511C MET* 1.3 65.7 + - + +
514C GLN* 2.8 45.2 + - - +
515C LEU* 3.0 46.1 + - + +
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Residues in contact with MET 511 (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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469C ARG* 3.9 33.9 - - + +
472C LEU* 3.9 32.3 - - + -
473C LEU* 4.1 19.3 - - + -
476C LEU* 4.1 21.1 - - - -
507C ILE* 2.9 26.4 + - - +
508C ALA* 3.4 9.2 - - - +
510C ASN* 1.3 75.7 - - - +
512C VAL* 1.3 59.2 + - - +
515C LEU* 3.6 9.1 + - + -
516C GLY 3.3 10.2 + - - -
517C MET* 2.9 41.5 + - + +
560C ILE* 4.3 17.7 - - + -
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Residues in contact with VAL 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ALA 3.1 14.9 + - - +
509C ARG 3.9 2.0 - - - +
511C MET* 1.3 82.2 - - - +
513C CYS* 1.3 70.2 + - - +
516C GLY* 4.4 6.4 + - - -
518C SER* 3.8 23.5 + - - +
521C LEU* 3.2 37.0 - - + +
522C GLY 5.1 0.9 - - - +
524C LEU 4.2 4.2 - - - +
526C TRP* 4.2 9.7 - - - -
553C ILE* 4.3 9.6 - - + +
556C GLU* 4.2 12.3 - - + -
557C VAL* 4.4 9.2 - - + -
560C ILE* 3.9 21.3 - - + -
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Residues in contact with CYS 513 (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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509C ARG* 2.7 37.7 + - - +
512C VAL* 1.3 75.9 - - - +
514C GLN* 1.3 72.2 + - - +
524C LEU 4.2 3.1 - - - -
525C ALA* 3.4 5.5 - - - +
526C TRP* 3.0 50.4 + - - +
545C TYR* 5.2 0.2 - - - -
553C ILE* 3.8 40.8 - - - -
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Residues in contact with GLN 514 (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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509C ARG 4.3 1.0 - - - +
510C ASN* 2.8 44.5 + - - +
512C VAL 3.5 0.2 - - - -
513C CYS* 1.3 92.9 - - - +
515C LEU* 1.3 74.3 + - + +
516C GLY 3.4 2.1 + - - -
524C LEU 5.2 3.0 - - - +
525C ALA* 5.0 9.0 - - + +
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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