Contacts of the strand formed by residues 622 - 629 (chain A) in PDB entry 4XUF
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 GLY 622 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A GLY 2.6 34.2 + - - +
620A ALA 3.8 0.2 - - - -
621A PHE* 1.3 82.0 - - - +
623A LYS* 1.3 63.7 + - - +
645A MET 3.3 12.1 - - - -
646A LEU* 3.7 5.8 - - - -
647A LYS* 3.6 4.2 - - - +
832A LEU 3.0 20.8 + - - +
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Residues in contact with LYS 623 (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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615A VAL* 4.2 24.4 - - + +
617A GLY 3.7 5.8 - - - +
618A SER* 3.6 25.8 + - - -
619A GLY 5.3 2.5 - - - +
622A GLY* 1.3 81.2 - - - +
624A VAL* 1.3 67.2 + - - +
625A MET* 4.2 7.4 - - + -
644A LYS* 4.7 1.1 - - - +
645A MET* 2.8 46.5 + - + +
647A LYS* 3.7 47.0 - - + +
832A LEU 3.9 0.2 + - - -
833A ALA* 5.1 1.3 - - - +
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Residues in contact with VAL 624 (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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615A VAL* 3.6 1.4 - - - +
616A LEU* 2.6 42.4 + - + -
617A GLY 2.9 14.1 + - - +
623A LYS* 1.3 74.2 - - - +
625A MET* 1.3 61.6 + - - +
642A ALA* 4.6 6.3 - - + -
643A VAL 3.4 11.7 - - - +
644A LYS* 3.5 32.1 - - + -
830A PHE* 5.1 2.5 - - + -
833A ALA* 3.6 19.5 - - + -
1001A P30 3.8 39.3 - - + +
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Residues in contact with MET 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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612A PHE* 3.9 28.7 - - + -
613A GLY 3.3 26.2 - - - +
614A LYS 3.6 4.9 - - - +
615A VAL* 3.7 31.4 - - + -
616A LEU* 3.9 6.5 - - - +
623A LYS* 4.8 5.2 - - + -
624A VAL* 1.3 79.8 - - - +
626A ASN* 1.3 63.9 + - - +
642A ALA* 3.8 5.0 - - - -
643A VAL* 3.0 32.4 + - - +
645A MET* 3.7 36.1 - - + +
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Residues in contact with ASN 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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612A PHE* 3.6 1.0 - - - -
613A GLY* 2.7 27.5 + - - -
614A LYS* 3.0 22.5 + - + +
616A LEU* 3.7 19.2 - - + +
625A MET* 1.3 74.6 - - - +
627A ALA* 1.3 82.4 + - - +
640A GLN* 3.0 26.4 + - - +
641A VAL 3.6 7.2 - - - +
693A TYR* 3.3 35.9 + - - -
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Residues in contact with ALA 627 (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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610A LEU* 3.5 30.1 - - + -
611A GLU 3.3 7.4 - - - +
612A PHE* 4.2 3.1 - - + -
613A GLY* 4.5 0.7 - - - +
626A ASN* 1.3 84.1 + - - +
628A THR* 1.3 64.7 + - - +
640A GLN* 3.1 9.1 - - - +
641A VAL* 3.0 35.3 + - + +
643A VAL* 3.6 19.5 - - + -
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Residues in contact with THR 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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609A ASN 3.6 0.2 - - - +
610A LEU* 4.9 0.4 - - - -
611A GLU* 2.8 47.3 + - - +
627A ALA* 1.3 73.8 - - - +
629A ALA* 1.3 57.9 + - - +
630A TYR* 3.5 20.9 - - - +
638A SER* 3.2 34.5 - - - +
639A ILE 3.5 8.1 - - - +
640A GLN* 3.9 15.1 + - - +
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Residues in contact with ALA 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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605A PHE* 4.4 12.3 - - + -
609A ASN 3.7 4.3 - - - -
610A LEU* 5.0 4.0 - - + +
627A ALA 4.0 0.6 - - - -
628A THR* 1.3 71.8 - - - +
630A TYR* 1.3 60.6 + - - +
631A GLY 3.9 1.4 + - - -
632A ILE* 4.1 24.9 - - + +
638A SER* 3.2 20.4 - - - -
639A ILE 3.1 13.7 + - - +
641A VAL* 3.9 30.1 - - + -
690A ILE* 5.2 3.6 - - + -
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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