Contacts of the strand formed by residues 628 - 633 (chain A) in PDB entry 1GEN
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 HIS 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A ASP* 3.3 21.5 - - - +
623A LEU 4.0 1.4 + - - +
626A GLY* 3.1 26.1 + - - -
627A GLY* 1.3 78.8 - - - +
629A SER* 1.3 61.8 + - - +
630A TYR* 3.8 30.9 + - + +
639A LYS* 3.5 37.1 + - + -
640A LEU 3.0 13.5 - - - +
641A GLU* 3.0 42.8 + - - -
642A ASN* 3.5 2.2 - - - +
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Residues in contact with SER 629 (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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572A PHE* 3.4 16.3 - - - -
574A TRP* 3.2 20.3 + - - -
620A VAL* 4.9 0.4 - - - -
621A VAL 3.6 5.4 - - - -
622A ASP* 3.5 3.0 + - - +
628A HIS* 1.3 72.3 - - - +
630A TYR* 1.3 61.7 + - - +
631A PHE* 3.7 22.2 - - - -
638A LEU 3.6 0.5 - - - +
639A LYS* 3.5 2.9 - - - -
640A LEU* 2.9 40.4 + - - +
642A ASN* 2.8 17.0 + - - -
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Residues in contact with TYR 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PRO* 5.8 1.8 - - + +
620A VAL* 3.2 25.3 - - - +
621A VAL* 2.9 22.8 + - + +
623A LEU* 3.9 26.7 - - + +
628A HIS* 3.8 28.9 + - + +
629A SER* 1.3 76.9 - - - +
631A PHE* 1.3 63.2 + - - +
632A PHE* 3.5 23.2 - - + -
637A TYR* 3.6 21.8 - + + -
638A LEU 3.2 4.5 - - - +
639A LYS* 3.7 40.8 + - + -
657A TRP* 3.5 28.9 - + - -
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Residues in contact with PHE 631 (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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572A PHE* 4.4 4.9 - + - -
583A PHE* 3.8 24.9 - + - -
610A TRP* 3.9 28.3 - + - -
613A ILE* 3.5 42.4 - - + -
617A LEU* 3.6 24.2 - - + -
619A ALA 3.9 3.4 - - - -
620A VAL* 3.7 15.5 - - + -
629A SER* 3.7 22.9 - - - -
630A TYR* 1.3 76.3 - - - +
632A PHE* 1.3 61.2 + - - +
633A LYS* 4.0 0.6 + - - +
636A TYR* 5.4 0.5 - - - -
637A TYR* 3.0 3.3 - - - -
638A LEU* 2.7 53.5 + - + +
640A LEU* 4.0 14.1 - - + -
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Residues in contact with PHE 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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478A ILE* 3.8 28.3 - - + -
617A LEU* 3.9 2.9 - - - +
618A ASP* 2.9 30.7 + - + +
619A ALA* 2.9 30.4 + - + +
621A VAL* 3.9 13.0 - - + -
630A TYR* 3.5 29.8 - - + -
631A PHE* 1.3 73.4 - - - +
633A LYS* 1.3 61.0 + - - +
636A TYR 3.7 1.8 - - - -
637A TYR* 3.7 20.2 - - + -
653A ILE* 3.7 24.5 - - + -
657A TRP* 3.6 48.9 - + - -
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Residues in contact with LYS 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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614A PRO* 3.8 21.9 - - + +
615A ASP 2.9 22.6 + - - +
616A ASN* 3.3 28.8 - - - +
617A LEU* 4.5 3.4 - - + -
618A ASP* 3.3 5.6 - - - +
631A PHE 4.0 0.8 + - - -
632A PHE* 1.3 76.9 - - - +
634A GLY* 1.3 70.0 + - - +
636A TYR* 2.8 69.6 + - + +
637A TYR* 4.7 0.2 - - - +
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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