Contacts of the helix formed by residues 581 - 586 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B ARG 3.9 5.5 + - - -
566B ILE* 4.7 6.6 - - - +
577B MET* 4.2 4.3 - - - -
579B VAL* 3.4 10.4 - - - +
580B SER* 1.3 83.4 - - - +
582B GLY* 1.3 62.2 + - - +
583B LEU* 3.0 26.4 + - - +
584B GLU* 3.1 8.1 + - - +
585B LEU* 3.0 16.8 + - - +
754B ALA* 3.5 30.7 + - - +
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Residues in contact with GLY 582 (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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564B ALA 3.1 22.9 - - - -
565B ARG* 3.0 25.3 + - - +
577B MET* 4.3 3.7 - - - +
580B SER 4.2 0.2 + - - -
581B SER* 1.3 73.1 - - - +
583B LEU* 1.3 60.9 + - - +
585B LEU* 3.2 10.0 + - - +
586B ILE* 3.1 30.3 + - - +
594B LEU* 4.1 5.8 - - - -
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Residues in contact with LEU 583 (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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564B ALA* 4.0 5.8 + - + -
566B ILE* 3.9 25.4 - - + -
581B SER* 3.0 10.5 + - - +
582B GLY* 1.3 78.9 - - - +
584B GLU* 1.3 61.2 + - - +
586B ILE* 3.5 8.4 - - + +
587B THR* 3.7 3.8 - - - +
598B ILE* 6.2 0.4 - - + -
708B PRO* 3.8 19.7 - - + -
710B LEU* 3.8 33.9 - - + -
750B MET* 3.3 33.3 - - + +
751B ALA* 4.5 2.0 - - - -
754B ALA* 4.4 7.6 - - + +
757B TYR* 3.5 44.6 - - + -
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Residues in contact with GLU 584 (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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579B VAL* 3.5 32.7 - - + +
580B SER* 5.1 2.6 + - - -
581B SER* 3.1 16.4 + - - +
583B LEU* 1.3 79.4 - - - +
585B LEU* 1.3 63.0 + - - +
587B THR* 2.8 24.8 + - - +
588B LEU* 3.5 11.2 - - + +
751B ALA* 3.6 37.4 - - + +
754B ALA* 4.6 4.0 - - + +
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Residues in contact with LEU 585 (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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565B ARG* 3.9 24.0 - - - +
577B MET* 3.9 27.6 - - + +
579B VAL* 3.9 11.2 - - + +
581B SER 3.0 12.8 + - - +
582B GLY* 3.2 11.9 + - - +
584B GLU* 1.3 76.7 - - - +
586B ILE* 1.3 58.2 + - - +
588B LEU* 2.9 26.3 + - + +
590B HIS* 3.6 39.9 - - + +
591B GLY* 3.3 24.5 - - - +
594B LEU* 4.5 11.9 - - + -
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Residues in contact with ILE 586 (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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582B GLY 3.1 5.5 + - - +
583B LEU* 3.5 18.4 - - + +
585B LEU* 1.3 75.0 - - - +
587B THR* 1.3 58.1 + - + +
588B LEU 3.2 1.6 - - - -
591B GLY* 4.2 2.0 - - - -
594B LEU* 3.1 41.3 - - + -
595B ARG* 2.7 42.9 + - + +
598B ILE* 4.2 11.7 - - + -
710B LEU* 3.7 29.2 - - + -
713B LEU* 4.7 5.1 - - + +
714B VAL* 4.3 14.6 - - + -
717B MET* 3.5 12.1 - - - +
750B MET* 3.9 14.4 - - + -
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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