Contacts of the strand formed by residues 619 - 627 (chain A) in PDB entry 6UMW
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 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A ILE* 3.9 15.9 - - + -
615A ASP 4.2 4.0 - - - +
616A VAL* 3.1 24.4 + - + +
617A SER 3.3 2.6 - - - +
618A PHE* 1.3 82.7 - - - +
620A LYS* 1.3 65.1 + - - +
621A ILE* 4.1 12.8 + - + +
637A ARG 3.4 6.7 - - - +
638A LEU* 3.8 19.7 - - + -
648A VAL* 5.2 1.3 - - + -
650A ILE* 3.6 34.8 - - + -
687A VAL* 5.0 3.6 - - + -
694A MET* 5.2 2.9 - - - -
696A ILE* 4.4 15.7 - - + -
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Residues in contact with LYS 620 (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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617A SER 5.5 5.8 - - - +
618A PHE 5.3 2.7 - - - +
619A VAL* 1.3 78.4 - - - +
621A ILE* 1.3 62.3 + - - +
622A GLU* 3.7 5.9 + - + +
636A GLY* 3.0 5.9 - - - -
637A ARG* 2.9 49.7 + - + +
645A GLU* 6.1 0.2 - - - +
650A ILE* 4.1 0.9 - - - +
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Residues in contact with ILE 621 (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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616A VAL* 5.8 2.9 - - + -
619A VAL* 4.1 8.7 - - + +
620A LYS* 1.3 74.7 - - - +
622A GLU* 1.3 62.7 + - - +
634A TYR* 3.4 49.8 - - + -
650A ILE* 3.8 19.7 - - + -
652A THR* 5.8 1.8 - - + -
694A MET* 4.0 31.0 - - + -
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Residues in contact with GLU 622 (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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620A LYS* 4.2 13.1 - - + +
621A ILE* 1.3 79.9 - - - +
623A GLU* 1.3 81.4 + - - +
624A VAL* 3.7 0.5 + - - +
634A TYR* 3.6 13.3 - - - -
635A LYS* 2.8 25.8 + - - +
636A GLY* 4.3 2.2 - - - -
637A ARG* 2.4 44.4 + - - -
647A PTR 4.1 12.8 + - - -
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Residues in contact with GLU 623 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A GLU* 1.3 88.7 - - - +
624A VAL* 1.3 64.7 + - - +
625A ILE* 3.9 17.1 - - + +
634A TYR* 3.3 1.8 - - - -
635A LYS* 2.8 58.2 + - + +
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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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622A GLU 5.1 0.7 - - - +
623A GLU* 1.3 81.6 - - - +
625A ILE* 1.3 64.2 + - - +
626A GLY 3.7 18.6 - - - +
627A ALA* 6.0 0.7 - - + -
632A GLU* 4.1 15.5 - - + -
633A VAL 3.6 13.0 - - - +
634A TYR* 3.5 23.8 - - + +
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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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623A GLU* 3.7 20.4 - - + +
624A VAL* 1.3 80.2 - - - +
626A GLY* 1.3 58.0 + - - +
633A VAL* 2.9 31.8 + - + +
634A TYR 3.9 5.4 - - - +
635A LYS* 3.8 24.7 - - + +
649A ALA* 4.6 0.4 - - + -
699A PHE* 3.9 15.3 - - + -
901A CTC 3.8 59.2 - - + +
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Residues in contact with GLY 626 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A VAL* 3.6 12.6 - - - +
625A ILE* 1.3 82.2 - - - +
627A ALA* 1.3 60.2 + - - -
628A GLY 3.8 2.2 - - - -
632A GLU* 3.5 3.1 - - - +
633A VAL* 2.8 32.0 + - - +
901A CTC 4.8 5.4 - - - -
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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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624A VAL* 6.0 0.4 - - + -
626A GLY* 1.3 72.3 - - - -
628A GLY* 1.3 66.1 + - - +
631A GLY 3.5 4.7 - - - -
632A GLU* 3.8 21.5 - - + +
654A LYS* 4.2 8.1 - - - +
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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