Contacts of the helix formed by residues 654 - 662 (chain A) in PDB entry 5YPO
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 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A PRO 3.2 2.2 + - - -
653A ARG* 1.3 81.4 - - - +
655A LEU* 1.3 64.6 + - - +
656A GLU* 3.2 21.7 + - - +
657A ASN* 3.0 24.3 + - - +
658A VAL* 3.0 16.3 + - - +
674A PHE* 3.3 19.3 - - - -
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Residues in contact with LEU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A SER* 1.3 74.2 - - - +
656A GLU* 1.3 71.5 + - + +
658A VAL* 3.1 16.2 + - + +
659A LEU* 3.3 17.7 + - + +
667A GLU* 4.0 23.3 - - + +
670A ALA* 3.6 17.9 - - + +
671A ARG* 3.4 61.5 - - + +
674A PHE* 3.8 20.9 - - + -
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Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A SER* 3.2 22.0 + - - +
655A LEU* 1.3 83.0 + - + +
657A ASN* 1.3 61.9 + - - +
659A LEU* 3.1 21.5 + - + +
660A GLU* 3.1 22.0 + - - +
666B THR* 6.5 1.1 - - + -
669B GLN* 3.4 27.4 + - - +
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Residues in contact with ASN 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ARG 4.3 1.0 - - - +
652A PRO* 3.3 7.6 - - - +
653A ARG* 2.7 37.1 + - + +
654A SER* 3.0 25.4 + - - +
656A GLU* 1.3 76.1 - - - +
658A VAL* 1.3 64.9 + - - +
660A GLU* 3.1 24.4 + - - +
661A ILE* 2.9 28.7 + - - +
693A GLU* 5.9 0.2 - - - +
694A GLY 2.9 29.6 + - - +
695A ASP* 3.7 5.9 + - - +
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Residues in contact with VAL 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A PRO* 4.5 14.1 - - + -
652A PRO* 3.5 26.7 - - + +
654A SER 3.0 15.4 + - - +
655A LEU* 3.1 8.7 + - - +
657A ASN* 1.3 75.3 - - - +
659A LEU* 1.3 56.8 + - - +
661A ILE* 3.3 5.4 + - - +
662A ASN* 2.8 29.4 + - + +
665A ILE* 4.1 10.8 - - + -
670A ALA* 3.6 30.5 - - + +
673A ALA* 4.3 9.4 - - + -
674A PHE* 3.9 23.1 - - + +
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Residues in contact with LEU 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 3.3 15.0 + - + +
656A GLU* 3.1 14.3 + - + +
658A VAL* 1.3 74.3 - - - +
660A GLU* 1.3 65.7 + - + +
662A ASN 3.3 17.1 - - - +
663A LYS* 3.6 13.9 - - - +
665A ILE* 3.8 24.7 - - + +
667A GLU* 4.1 33.0 - - + +
670A ALA* 3.7 23.6 - - + -
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A GLU* 3.1 17.4 + - - +
657A ASN* 3.1 32.1 + - - +
659A LEU* 1.3 77.5 - - + +
661A ILE* 1.3 63.0 + - - +
663A LYS* 3.8 25.9 + - - +
695A ASP* 3.4 38.6 - - - +
696A SER* 3.8 5.9 - - - -
697A PHE 4.5 0.2 + - - -
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Residues in contact with ILE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A PRO* 4.3 11.7 - - + +
543A THR* 3.6 27.9 - - + +
546A ARG* 5.2 1.4 + - - -
650A ILE* 4.8 7.0 - - + -
651A ARG 5.3 1.1 - - - +
652A PRO* 4.7 11.9 - - + -
657A ASN* 2.9 32.2 + - - +
658A VAL* 3.8 4.0 - - - +
660A GLU* 1.3 78.7 - - - +
662A ASN* 1.3 58.8 + - + +
663A LYS* 3.9 2.6 + - - +
694A GLY 3.3 31.6 - - - +
696A SER 4.2 3.4 - - - +
697A PHE* 3.5 30.4 + - - +
700A ILE* 4.0 29.6 - - + -
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Residues in contact with ASN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A PRO* 5.2 3.6 - - + +
543A THR* 3.5 30.3 - - + +
546A ARG* 6.0 1.1 + - - +
658A VAL* 2.8 20.4 + - + +
659A LEU* 3.3 14.1 - - - +
661A ILE* 1.3 72.0 - - + +
663A LYS* 1.3 57.3 + - - +
664A ARG* 3.0 30.0 + - - +
665A ILE* 3.5 45.1 + - + +
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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