Contacts of the helix formed by residues 3477 - 3490 (chain C) in PDB entry 5Y3R
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 GLU3477 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3476C PRO* 1.3 81.8 - - + +
3478C GLU* 1.3 54.9 + - - +
3480C LEU* 2.7 16.0 + - + -
3481C SER* 2.1 72.8 + - - +
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Residues in contact with GLU3478 (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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3444C ALA* 3.0 35.2 - - - +
3447C VAL* 6.1 2.5 - - + -
3475C TYR* 2.9 45.4 + - + -
3476C PRO* 3.5 1.6 - - + +
3477C GLU* 1.3 79.1 - - - +
3479C THR* 1.3 67.1 + - - +
3481C SER* 2.9 13.9 + - - -
3482C LEU* 3.0 35.1 + - + +
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Residues in contact with THR3479 (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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3447C VAL* 6.1 0.7 - - - -
3465C PHE 5.3 0.5 + - - -
3469C LEU* 3.5 28.1 + - + +
3473C GLU* 3.1 24.7 + - - +
3475C TYR* 2.9 24.5 + - - +
3476C PRO 3.5 7.6 - - - +
3478C GLU* 1.3 80.1 - - - +
3480C LEU* 1.3 70.3 + - + +
3483C MET* 3.0 41.9 - - - +
3516C HIS* 2.8 23.0 + - - -
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Residues in contact with LEU3480 (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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3469C LEU* 3.9 13.2 - - + -
3476C PRO 3.1 23.8 - - - +
3477C GLU* 2.7 20.3 + - + +
3479C THR* 1.3 85.9 - - + +
3481C SER* 1.3 57.1 + - - +
3484C THR* 2.1 42.6 + - - +
3512C VAL* 4.1 9.6 - - + -
3515C GLN* 3.1 47.1 - - + +
3516C HIS* 3.0 32.5 - - + +
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Residues in contact with SER3481 (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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3477C GLU* 2.1 65.6 + - - +
3478C GLU* 2.9 6.7 + - - -
3480C LEU* 1.3 72.7 - - - +
3482C LEU* 1.3 65.8 + - - -
3484C THR* 3.4 2.3 - - - +
3485C LYS* 2.9 41.3 + - - +
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Residues in contact with LEU3482 (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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3444C ALA 5.2 2.2 - - - +
3447C VAL* 5.8 3.1 - - + -
3448C GLU* 3.2 62.1 - - + +
3451C LEU* 5.8 3.4 - - + -
3478C GLU* 3.0 30.5 + - + +
3481C SER* 1.3 81.5 - - - +
3483C MET* 1.3 60.9 + - + +
3485C LYS* 2.6 57.4 + - + +
3486C GLU* 3.1 4.4 + - - +
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Residues in contact with MET3483 (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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3447C VAL* 4.0 26.9 - - + +
3448C GLU* 5.9 0.4 - - - -
3465C PHE* 3.3 42.2 - - + +
3468C LEU* 4.1 18.2 - - + -
3478C GLU 4.2 0.2 + - - -
3479C THR* 3.0 56.5 + - - +
3482C LEU* 1.3 78.6 - - + +
3484C THR* 1.3 49.5 + - - +
3486C GLU* 2.4 44.5 + - + +
3516C HIS* 3.1 13.7 - - + +
3520C GLU* 2.4 20.1 - - - +
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Residues in contact with THR3484 (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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3480C LEU* 2.1 30.5 + - - -
3481C SER 3.4 2.2 - - - +
3483C MET* 1.3 73.0 - - - +
3485C LYS* 1.3 57.5 + - + +
3486C GLU 3.1 0.9 + - - -
3488C SER* 2.5 31.7 + - - +
3515C GLN 3.4 3.3 + - - +
3516C HIS* 2.2 39.0 + - - -
3519C GLU* 3.4 35.7 - - + +
3520C GLU* 3.2 11.0 - - - +
3523C ASP* 5.3 0.2 - - - +
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Residues in contact with LYS3485 (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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3451C LEU* 5.7 14.7 - - + +
3481C SER* 2.9 32.2 + - - +
3482C LEU* 2.6 40.9 + - + +
3484C THR* 1.3 73.3 - - + +
3486C GLU* 1.3 53.2 + - - +
3488C SER* 4.2 3.8 - - - -
3489C SER* 2.4 44.4 + - - -
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Residues in contact with GLU3486 (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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3450C MET* 3.5 24.3 - - + +
3454C LEU* 4.7 5.3 - - - +
3462C ARG* 5.5 1.1 - - - -
3465C PHE* 3.1 34.0 - - - +
3482C LEU 3.1 4.1 + - - +
3483C MET* 2.4 56.2 + - + +
3484C THR 3.0 0.8 - - - -
3485C LYS* 1.3 64.2 - - - +
3487C ILE* 1.3 61.9 + - + +
3489C SER 2.6 7.1 + - - -
3490C VAL* 2.3 45.3 + - + +
3498C TRP* 3.9 23.6 - - - -
3520C GLU* 3.9 4.6 - - - +
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Residues in contact with ILE3487 (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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3454C LEU* 4.4 3.8 - - + -
3486C GLU* 1.3 86.0 - - + +
3488C SER* 1.3 55.9 - - - +
3490C VAL* 2.8 29.8 - - + +
3491C PRO 3.1 19.5 - - - +
3492C CYS 3.3 10.5 - - - +
3494C GLN* 3.4 9.4 - - + -
3495C PHE* 3.2 44.9 - - + +
3498C TRP* 3.5 17.0 - - + -
3520C GLU* 3.2 21.5 + - + +
3524C ASN* 2.3 39.7 + - - +
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Residues in contact with SER3488 (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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3484C THR* 2.5 30.1 + - - +
3485C LYS* 4.0 4.7 - - - -
3487C ILE* 1.3 79.4 - - - +
3489C SER* 1.3 64.4 + - - +
3490C VAL 3.7 0.3 - - - +
3519C GLU 4.1 0.2 - - - -
3520C GLU* 3.0 14.9 + - - +
3523C ASP* 2.4 42.7 + - - +
3524C ASN* 3.8 4.7 + - - -
3527C GLN* 4.9 7.8 - - - +
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Residues in contact with SER3489 (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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3451C LEU* 4.5 15.7 - - - +
3485C LYS* 2.4 36.1 + - - -
3486C GLU* 2.6 7.0 + - - -
3488C SER* 1.3 73.3 - - - +
3490C VAL* 1.3 71.8 + - - +
3491C PRO* 3.6 2.4 - - - +
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Residues in contact with VAL3490 (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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3450C MET* 3.9 16.4 - - + +
3451C LEU* 5.2 6.3 - - + +
3454C LEU* 3.5 28.5 - - + -
3486C GLU* 2.3 45.0 + - - +
3487C ILE* 2.8 26.1 - - + +
3488C SER 3.7 0.5 - - - +
3489C SER* 1.3 78.3 - - - +
3491C PRO* 1.3 80.0 - - + +
3492C CYS 3.4 0.3 + - - -
3494C GLN* 3.4 22.2 - - + -
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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