Contacts of the helix formed by residues 623 - 628 (chain B) in PDB entry 5SY1
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 VAL 623 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616B LEU* 3.8 34.3 - - + +
619B ASN 4.1 0.7 - - - +
620B PRO* 3.2 18.5 + - + +
622B LEU* 1.3 77.4 - - - +
624B GLY* 1.3 58.5 + - - +
626B ARG* 3.2 7.0 + - + +
627B LYS* 3.0 55.2 + - + +
112D ASN 5.3 0.4 - - - +
113D LEU* 3.7 36.1 - - + -
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Residues in contact with GLY 624 (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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620B PRO 4.6 0.4 + - - -
621B SER 4.1 5.6 + - - -
622B LEU 3.3 0.2 - - - -
623B VAL* 1.3 79.6 - - - +
625B SER* 1.3 56.7 + - - +
627B LYS* 4.6 2.7 - - - -
628B HIS* 2.9 52.1 + - - -
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Residues in contact with SER 625 (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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621B SER 3.9 6.9 + - - -
622B LEU* 3.0 35.9 + - - +
624B GLY* 1.3 74.4 - - - +
626B ARG* 1.3 58.2 + - - +
628B HIS* 4.8 2.5 - - - +
629B PHE* 3.3 39.9 - - - +
14D LYS* 4.8 11.1 + - - -
65D ASP* 4.3 3.6 - - - +
66D PHE* 5.3 4.2 - - - +
67D PRO* 4.8 4.3 - - - +
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Residues in contact with ARG 626 (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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612B LEU* 4.5 26.5 - - - +
616B LEU* 3.7 31.7 - - + +
622B LEU 2.5 18.4 + - - +
623B VAL* 3.6 8.3 - - - +
624B GLY 3.2 0.4 - - - -
625B SER* 1.3 74.8 - - - +
627B LYS* 1.3 65.2 + - + +
628B HIS 3.3 0.2 - - - -
629B PHE 3.1 2.3 + - - -
630B GLN* 2.7 46.4 + - + +
59D ASP* 5.1 3.4 - - - +
65D ASP* 3.3 21.9 + - - +
67D PRO* 4.0 16.3 - - + +
68D GLU* 5.3 5.1 + - - +
113D LEU 5.0 8.1 + - - -
116D LYS* 3.0 50.7 - - - +
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Residues in contact with LYS 627 (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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623B VAL* 3.0 34.4 + - + +
624B GLY* 4.3 2.5 - - - +
626B ARG* 1.3 85.6 - - + +
628B HIS* 1.3 69.5 + - + +
630B GLN* 3.3 39.4 + - - +
112D ASN 4.2 4.9 + - - -
113D LEU* 3.2 26.9 - - - +
114D GLY* 3.1 28.9 - - - +
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Residues in contact with HIS 628 (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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624B GLY* 2.9 30.6 + - - +
625B SER* 4.8 2.4 - - - -
627B LYS* 1.3 83.3 - - + +
629B PHE* 1.3 74.7 + - + +
630B GLN 3.6 1.5 + - - +
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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