Contacts of the strand formed by residues 624 - 628 (chain A) in PDB entry 3QER
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 624 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A SER* 6.1 0.4 - - - -
410A PHE 3.2 11.0 - - - -
411A ASP* 4.0 13.7 - - - -
594A LEU* 3.2 9.1 - - - +
620A GLY* 3.0 19.1 - - - -
621A ASP* 3.3 23.4 + - - +
623A ASP* 1.3 80.3 - - - +
625A ILE* 1.3 63.4 + - - +
626A TYR* 3.6 23.3 + - - -
683A MET* 4.4 0.4 - - - -
686A GLU* 5.8 2.0 - - - -
906A CA 4.0 4.9 - - - -
115P DOC 5.3 3.2 + - - -
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Residues in contact with ILE 625 (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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408A MET 4.1 0.7 - - - +
409A SER* 3.2 5.5 - - - -
410A PHE* 2.9 57.6 + - + +
594A LEU* 3.6 21.1 - - + +
597A ILE* 4.3 13.2 - - + -
598A GLU* 4.7 5.8 - - + -
601A VAL* 3.8 31.6 - - + -
617A VAL* 4.0 20.9 - - + -
619A TYR 3.5 4.5 - - - +
620A GLY* 5.0 0.7 - - - -
624A SER* 1.3 78.1 - - - +
626A TYR* 1.3 64.1 + - - +
627A VAL* 3.8 19.3 - - + -
663A ILE* 4.7 0.7 - - + -
683A MET* 4.0 12.6 - - + -
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Residues in contact with TYR 626 (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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407A VAL* 3.9 9.2 - - + -
408A MET 3.8 1.6 - - - -
409A SER* 3.5 24.2 - - - -
617A VAL* 3.4 2.8 - - - -
618A LEU* 2.8 39.1 + - + +
619A TYR* 2.8 40.5 + + + +
624A SER* 3.6 27.7 + - - -
625A ILE* 1.3 75.2 - - - +
627A VAL* 1.3 62.3 + - - +
686A GLU* 4.5 7.3 + - - -
687A ALA* 5.8 0.2 - - + -
702A TRP* 3.6 30.3 - + + -
708A TYR* 2.7 32.5 + + - -
710A LEU* 3.9 17.9 - - + -
726A LYS* 4.1 11.3 - - - -
115P DOC 4.2 2.5 + - - -
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Residues in contact with VAL 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A VAL* 3.3 2.8 - - - +
408A MET* 2.8 51.0 + - + +
410A PHE* 4.1 11.9 - - + -
601A VAL* 4.2 11.2 - - + -
605A LEU* 3.5 29.4 - - + -
616A PHE* 3.5 10.5 - - + +
617A VAL* 4.4 4.0 - - + -
618A LEU* 4.1 2.7 - - - -
625A ILE* 3.8 27.6 - - + -
626A TYR* 1.3 75.7 - - - +
628A SER* 1.3 73.9 + - - +
629A ALA* 3.3 1.5 + - + -
632A ILE* 5.1 5.2 - - + -
659A MET* 4.2 6.5 - - + -
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Residues in contact with SER 628 (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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404A TYR* 4.8 11.3 - - - +
406A TYR 3.5 6.4 + - - -
615A ALA 5.1 3.6 - - - -
616A PHE* 2.8 45.3 + - - -
618A LEU* 3.7 19.3 - - - +
627A VAL* 1.3 73.1 - - - +
629A ALA* 1.3 59.6 + - - +
630A ASP* 3.4 25.6 + - - +
631A LYS* 4.9 0.9 + - - +
632A ILE* 4.7 0.7 - - - +
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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