Contacts of the helix formed by residues 581 - 586 (chain C) in PDB entry 3T6A
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 SER 581 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565C ARG 3.5 11.4 + - - -
566C ILE* 4.5 5.9 - - - +
577C MET* 4.5 3.6 - - - -
579C VAL* 3.4 10.6 + - - +
580C SER* 1.3 82.3 - - - +
582C GLY* 1.3 64.5 + - - +
583C LEU* 2.9 29.3 + - - +
584C GLU* 2.9 15.7 + - - +
585C LEU 3.1 7.8 + - - -
754C ALA* 3.8 27.8 + - - +
758C ARG* 6.2 2.2 - - - -
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Residues in contact with GLY 582 (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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564C ALA 3.2 17.9 - - - -
565C ARG* 2.9 23.6 + - - +
577C MET* 4.3 3.3 - - - -
581C SER* 1.3 70.8 - - - +
583C LEU* 1.3 57.6 + - - +
584C GLU 3.2 0.2 - - - -
585C LEU* 3.5 7.0 - - - +
586C ILE* 2.9 35.5 + - - +
594C LEU* 3.8 13.5 - - - -
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Residues in contact with LEU 583 (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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564C ALA* 4.1 9.2 + - + -
566C ILE* 3.7 27.4 - - + -
581C SER* 2.9 15.5 + - - +
582C GLY* 1.3 79.3 - - - +
584C GLU* 1.3 60.9 + - - +
586C ILE* 3.6 9.6 - - + +
587C THR* 3.5 7.1 - - - +
708C PRO* 3.9 25.6 - - + -
710C LEU* 4.3 15.3 - - + -
750C MET* 3.4 30.6 - - + +
751C ALA* 4.4 3.4 - - - -
754C ALA* 4.4 8.1 - - + +
757C TYR* 3.4 45.5 - - + -
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Residues in contact with GLU 584 (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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579C VAL* 3.9 32.1 - - + +
580C SER 5.2 2.1 + - - -
581C SER* 2.9 13.2 + - - +
583C LEU* 1.3 78.6 - - - +
585C LEU* 1.3 63.4 + - - +
587C THR* 2.7 25.5 + - - +
588C LEU* 3.6 11.7 - - + +
751C ALA* 3.6 35.9 - - + +
754C ALA* 4.5 8.6 - - + +
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Residues in contact with LEU 585 (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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565C ARG* 3.7 26.7 - - - +
577C MET* 3.9 20.9 - - + +
579C VAL* 4.0 13.9 - - + +
581C SER 3.1 6.6 + - - +
582C GLY* 3.1 14.3 + - - +
584C GLU* 1.3 77.6 - - - +
586C ILE* 1.3 61.4 + - - +
588C LEU* 3.2 28.4 + - + +
590C HIS* 4.4 13.2 - - + +
591C GLY* 3.3 29.9 + - - +
594C LEU* 4.3 16.2 - - + -
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Residues in contact with ILE 586 (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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582C GLY 2.9 21.2 + - - +
583C LEU* 3.6 22.9 - - + +
585C LEU* 1.3 74.4 - - - +
587C THR* 1.3 56.6 + - - +
588C LEU 3.2 0.9 - - - -
591C GLY* 4.4 1.8 - - - -
594C LEU* 3.4 30.5 - - + -
595C ARG* 2.5 41.3 + - + +
598C ILE* 4.0 21.1 - - + -
710C LEU* 3.6 31.2 - - + -
713C LEU* 5.0 5.4 - - + -
714C VAL* 4.5 8.5 - - + -
717C MET* 3.6 11.4 - - - +
750C MET* 4.2 9.6 - - + -
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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