Contacts of the helix formed by residues 608 - 612 (chain I) in PDB entry 6PSU
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 608 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447I HIS* 4.0 11.6 + - - -
448I LEU 3.1 36.4 + - - +
449I GLY* 3.8 2.0 - - - +
553I THR* 3.8 21.5 - - + +
557I ARG* 3.4 26.6 - - - +
587I LEU 3.7 1.6 + - - -
607I SER* 1.3 74.1 - - - +
609I ILE* 1.3 58.9 + - - +
610I GLU 3.1 3.1 + - - -
611I GLU* 3.9 9.2 + - - +
612I GLY 4.6 4.7 + - - -
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Residues in contact with ILE 609 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403I MET* 3.8 32.1 - - + -
404I LYS* 4.8 3.6 - - - +
407I ARG* 3.9 35.3 + - + +
447I HIS* 4.8 4.9 - - + -
448I LEU 5.0 0.2 - - - +
449I GLY* 3.4 37.2 - - - +
586I PHE* 5.0 12.1 - - + -
607I SER* 3.1 10.4 + - - +
608I ALA* 1.3 78.0 - - - +
610I GLU* 1.3 81.8 - - + +
612I GLY 5.3 0.2 - - - -
613I ASN* 4.0 8.9 - - - +
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Residues in contact with GLU 610 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407I ARG* 3.8 20.5 + - - +
588I GLU* 4.8 4.2 - - - +
606I LEU* 4.8 11.0 - - + -
607I SER* 2.1 42.5 + - - +
609I ILE* 1.3 96.1 - - - +
611I GLU* 1.3 54.5 + - - +
612I GLY 3.1 2.7 - - - -
613I ASN* 2.5 43.7 + - + +
614I TYR* 3.0 26.9 - - + +
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Residues in contact with GLU 611 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552I PRO 4.9 6.8 - - - +
553I THR* 5.3 1.6 - - - -
555I TYR* 4.8 1.2 - - - +
557I ARG* 2.5 49.5 + - - +
591I TYR* 3.6 8.4 + - + +
606I LEU* 5.3 6.0 - - + +
607I SER 3.3 4.7 + - - +
608I ALA* 3.9 6.0 + - - +
610I GLU* 1.3 76.2 - - - +
612I GLY* 1.3 60.6 + - - +
613I ASN 3.1 0.6 + - - -
614I TYR* 3.4 18.7 + - - +
616I ILE* 3.4 26.0 - - + +
637I ARG* 2.3 45.6 + - - +
638I SER 4.8 3.4 - - - +
639I LYS 4.6 1.7 + - - -
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Residues in contact with GLY 612 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608I ALA 4.6 4.6 + - - -
609I ILE 5.3 0.2 - - - -
610I GLU 3.0 1.8 + - - -
611I GLU* 1.3 78.6 - - - +
613I ASN* 1.3 62.9 + - - +
614I TYR 3.1 7.2 + - - +
638I SER* 5.2 0.3 - - - -
639I LYS* 3.4 50.3 + - - +
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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