Contacts of the helix formed by residues 631 - 641 (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 631 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LEU* 4.6 3.8 - - - -
600A GLU* 3.1 15.6 + - - -
630A VAL* 1.3 80.3 - - - +
632A ALA* 1.3 67.9 + - - +
633A ASN* 3.3 8.1 - - - -
634A ALA* 3.0 17.8 + - - +
635A VAL* 3.7 4.7 + - - +
3D LEU* 5.8 0.2 - - - +
6D THR* 4.0 9.9 + - - -
7D GLN* 3.2 39.3 + - - +
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Residues in contact with ALA 632 (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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540A LEU* 3.8 17.6 - - + +
631A SER* 1.3 75.8 - - - +
633A ASN* 1.3 64.1 + - - +
635A VAL* 2.9 22.7 + - - +
636A ARG* 3.9 2.1 + - - +
680A LEU* 3.7 21.1 - - + -
684A PHE* 3.6 43.4 - - + -
688A PHE* 5.7 0.2 - - + -
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Residues in contact with ASN 633 (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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631A SER* 3.3 5.4 - - - -
632A ALA* 1.3 76.8 - - - +
634A ALA* 1.3 63.1 + - - +
635A VAL 3.2 0.7 + - - -
636A ARG* 3.3 18.2 + - - +
637A ARG* 3.3 37.3 + - - +
684A PHE* 3.5 24.3 - - - -
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Residues in contact with ALA 634 (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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599A ILE* 3.6 24.0 - - + +
600A GLU* 4.0 10.7 + - + +
630A VAL* 3.6 26.0 - - + -
631A SER 3.0 14.7 + - - +
633A ASN* 1.3 76.0 - - - +
635A VAL* 1.3 58.5 + - - +
637A ARG* 3.3 11.4 + - - +
638A LEU* 2.9 34.9 + - + +
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Residues in contact with VAL 635 (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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538A ILE* 3.7 40.4 - - + -
540A LEU* 4.4 11.2 - - + -
631A SER 3.7 4.7 + - - +
632A ALA* 2.9 16.3 + - - +
634A ALA* 1.3 76.5 - - - +
636A ARG* 1.3 58.4 + - - +
638A LEU* 3.2 4.3 + - - +
639A GLN* 2.8 49.8 + - + +
645A PRO* 4.3 2.4 - - + +
647A ALA* 4.0 17.5 - - + -
687A CYS* 3.6 28.7 - - - -
688A PHE* 5.3 0.7 - - + -
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Residues in contact with ARG 636 (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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632A ALA 4.6 5.4 - - - +
633A ASN* 3.3 13.0 + - - +
635A VAL* 1.3 75.8 - - - +
637A ARG* 1.3 55.0 + - - +
639A GLN* 3.1 15.9 + - - +
640A ALA* 2.7 38.6 + - - +
683A GLU* 3.2 23.4 + - - +
684A PHE* 3.5 38.5 - - + +
686A GLU* 5.8 2.4 - - - +
687A CYS* 4.4 17.1 - - + +
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Residues in contact with ARG 637 (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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598A PHE 5.0 4.2 + - - +
599A ILE* 2.8 46.0 + - + +
600A GLU* 4.0 14.5 - - - +
601A ALA 5.3 3.6 + - - +
633A ASN* 3.3 32.0 + - - +
634A ALA* 3.3 25.3 + - - +
636A ARG* 1.3 79.3 - - - +
638A LEU* 1.3 58.0 + - - +
640A ALA* 3.3 4.0 + - - +
641A ALA* 2.8 33.5 + - - +
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Residues in contact with LEU 638 (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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536A PRO* 4.5 4.9 - - + -
538A ILE* 3.4 28.3 - - + -
599A ILE* 3.8 28.3 - - + -
616A VAL* 4.2 14.8 - - + -
628A LEU* 3.7 16.2 - - + -
634A ALA* 2.9 23.4 + - + +
635A VAL 3.6 3.4 - - - +
637A ARG* 1.3 76.0 - - - +
639A GLN* 1.3 61.5 + - - +
641A ALA* 3.5 5.1 + - - -
642A HIS 3.3 2.8 + - - -
643A LEU* 3.0 62.6 + - + +
645A PRO* 4.0 15.4 - - + +
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Residues in contact with GLN 639 (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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635A VAL* 2.8 25.1 + - - +
636A ARG* 3.1 19.3 + - - +
638A LEU* 1.3 75.8 - - - +
640A ALA* 1.3 58.3 + - - +
642A HIS* 2.8 26.2 + - - -
643A LEU 5.0 0.2 - - - +
644A HIS 5.2 0.6 + - - +
645A PRO* 3.7 24.7 + - + +
647A ALA* 5.0 2.8 - - - +
687A CYS* 2.8 41.1 + - - +
689A SER* 5.5 1.6 + - - -
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Residues in contact with ALA 640 (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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636A ARG 2.7 20.9 + - - +
637A ARG* 4.0 4.9 - - - +
639A GLN* 1.3 73.1 - - - +
641A ALA* 1.3 55.1 + - - +
642A HIS* 3.2 24.2 + - - -
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Residues in contact with ALA 641 (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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599A ILE* 6.0 1.6 - - + -
613A VAL* 5.7 10.3 - - + -
617A ARG* 5.3 1.4 + - - -
637A ARG 2.8 23.3 + - - +
638A LEU* 3.8 6.7 - - - +
639A GLN 3.1 0.4 - - - -
640A ALA* 1.3 70.7 - - - +
642A HIS* 1.3 76.4 + - - +
643A LEU* 3.1 21.5 - - + +
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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