Contacts of the helix formed by residues 480 - 492 (chain C) 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 LYS 480 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C ASP* 3.0 23.0 + - - -
446C VAL* 3.7 27.1 + - + +
448C THR* 3.4 32.3 - - - +
475C ALA* 3.6 15.9 - - + -
479C GLY* 1.3 72.4 - - - -
481C GLU* 1.3 60.5 + - - +
482C SER 3.3 0.7 - - - -
483C CYS* 2.9 20.5 + - - +
484C PHE* 2.9 31.9 + - + -
505C GLU* 2.9 34.1 + - + +
506C GLU* 2.9 42.1 + - + +
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Residues in contact with GLU 481 (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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478C THR 5.6 1.1 - - - +
479C GLY 3.6 0.4 - - - -
480C LYS* 1.3 77.0 - - - +
482C SER* 1.3 65.3 + - - +
484C PHE* 3.2 15.5 + - - +
485C GLU* 3.1 18.7 + - - +
505C GLU* 5.5 1.0 + - - +
509C GLY* 4.4 13.3 - - - -
512C LYS* 3.2 35.4 - - + +
513C HIS* 3.3 24.1 + - + +
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Residues in contact with SER 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C THR* 2.8 49.7 + - - +
480C LYS 3.3 0.4 - - - -
481C GLU* 1.3 80.9 - - - +
483C CYS* 1.3 57.8 + - - +
485C GLU* 3.5 16.3 + - - +
486C ARG* 3.1 28.1 + - - +
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Residues in contact with CYS 483 (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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331C ILE* 4.4 9.0 - - - -
446C VAL* 4.0 16.2 - - + -
473C TYR* 4.2 17.8 - - + -
474C SER 3.5 26.9 - - - -
475C ALA* 3.8 5.6 - - - -
478C THR* 3.5 17.9 - - - -
479C GLY 3.7 9.0 - - - +
480C LYS 2.9 12.8 + - - +
482C SER* 1.3 79.9 + - - +
484C PHE* 1.3 59.3 + - - +
486C ARG* 3.9 7.6 + - - +
487C ILE* 3.1 30.1 + - - +
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Residues in contact with PHE 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 3.5 34.5 - - + -
446C VAL* 3.9 20.0 - - + -
480C LYS* 2.9 29.5 + - + -
481C GLU* 3.4 6.5 - - - +
483C CYS* 1.3 78.5 - - - +
485C GLU* 1.3 66.8 + - - +
487C ILE* 2.8 17.2 + - - +
488C MET* 2.9 16.2 + - - +
499C VAL* 3.9 20.4 - - + -
506C GLU* 3.6 37.2 - - + -
509C GLY* 3.9 15.5 - - - -
510C ALA 4.1 0.7 - - - -
513C HIS* 4.8 1.8 - - + -
515C MET* 3.6 33.4 - - + -
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Residues in contact with GLU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C GLU* 3.1 5.7 + - - +
482C SER* 3.6 16.6 - - - +
484C PHE* 1.3 79.0 - - - +
486C ARG* 1.3 56.3 + - - +
488C MET* 3.1 7.8 + - + +
489C GLN* 2.9 61.1 + - - +
513C HIS* 3.5 30.6 + - + +
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Residues in contact with ARG 486 (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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331C ILE* 3.0 35.2 - - - +
332C HIS* 3.2 17.6 + - - +
335C ASP* 2.8 32.3 + - - -
473C TYR* 3.5 28.2 + - + +
482C SER 3.1 14.6 + - - +
483C CYS* 4.0 7.4 - - - +
484C PHE 3.2 0.2 - - - -
485C GLU* 1.3 80.0 - - - +
487C ILE* 1.3 56.2 + - - +
489C GLN* 3.7 11.4 + - - +
490C ARG* 3.1 24.1 + - + +
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Residues in contact with ILE 487 (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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270C VAL* 4.1 13.7 - - + -
272C VAL* 4.0 13.7 - - + -
444C VAL* 3.5 17.0 - - + -
446C VAL* 3.4 29.2 - - + -
473C TYR* 3.8 24.7 - - + -
483C CYS 3.1 20.4 - - - +
484C PHE* 2.8 9.9 + - - +
486C ARG* 1.3 75.5 - - - +
488C MET* 1.3 61.6 + - - +
490C ARG* 3.1 5.3 + - - +
491C PHE* 2.9 53.9 + - + +
497C TYR* 4.2 8.3 - - + -
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Residues in contact with MET 488 (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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484C PHE 2.9 11.2 + - - +
485C GLU* 3.5 8.5 - - - +
487C ILE* 1.3 76.2 - - - +
489C GLN* 1.3 61.2 + - - +
492C GLY 2.6 37.2 + - - +
493C ARG* 5.8 4.0 - - + -
497C TYR* 3.5 44.4 - - + -
513C HIS* 4.2 29.8 - - - +
514C ASN 5.7 0.9 - - - +
515C MET* 3.7 30.5 - - + +
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Residues in contact with GLN 489 (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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485C GLU* 2.9 53.8 + - - +
486C ARG* 4.0 9.2 - - - +
488C MET* 1.3 78.4 - - - +
490C ARG* 1.3 64.7 + - - +
492C GLY* 3.9 4.7 + - - -
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Residues in contact with ARG 490 (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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332C HIS* 4.4 1.4 + - - -
470C GLU* 2.7 40.0 + - - +
471C ASN* 3.9 13.7 + - - +
473C TYR* 3.0 27.8 + - - +
486C ARG* 3.1 15.1 + - + +
487C ILE* 3.1 11.5 + - - +
489C GLN* 1.3 79.3 - - - +
491C PHE* 1.3 98.0 + - + +
492C GLY* 3.4 0.7 + - - -
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Residues in contact with PHE 491 (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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268C GLU* 4.4 13.8 - - - +
270C VAL* 3.6 23.1 - - + -
442C VAL* 4.0 24.9 - - + -
444C VAL* 3.6 32.1 - - + -
471C ASN* 4.1 3.6 - - - -
473C TYR* 5.1 0.9 - - - -
487C ILE* 2.9 31.4 + - + -
490C ARG* 1.3 118.1 - - + +
492C GLY* 1.3 57.2 + - - +
494C LYS* 6.1 0.2 - - - +
495C ALA* 4.2 10.9 + - + +
497C TYR* 3.4 14.1 - - - +
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Residues in contact with GLY 492 (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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488C MET* 2.6 21.9 + - - +
489C GLN 4.4 4.0 - - - -
490C ARG 3.3 4.2 + - - -
491C PHE* 1.3 79.9 - - - +
493C ARG* 1.3 61.0 + - - -
494C LYS* 3.6 2.5 - - - -
495C ALA 4.5 0.7 - - - -
497C TYR* 2.4 29.5 + - - -
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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