Contacts of the strand formed by residues 621 - 626 (chain A) in PDB entry 1UUR
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 PHE 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A THR* 4.1 10.1 - - + -
573A LEU* 5.6 0.7 - - + -
576A GLN* 5.0 5.4 - - - -
579A ILE* 3.5 47.3 - - + -
583A TRP* 6.2 0.2 - + - -
588A ILE* 3.7 26.2 - - + -
611A ILE* 4.0 18.2 - - + -
612A ARG 3.2 17.7 - - - +
613A PHE* 3.4 35.0 - + - -
614A SER 4.5 0.2 - - - -
619A GLY 5.6 0.4 - - - -
620A GLN* 1.3 77.7 - - - +
622A GLY* 1.3 59.9 + - - +
623A ILE* 5.2 0.7 - - + +
638A LEU* 3.6 8.6 - - - +
639A VAL* 2.9 45.4 + - + +
651A PHE* 4.0 17.9 - + + -
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Residues in contact with GLY 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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612A ARG* 2.7 49.9 + - - -
614A SER* 4.3 4.8 - - - +
620A GLN 4.2 0.2 + - - -
621A PHE* 1.3 76.6 - - - +
623A ILE* 1.3 64.6 + - - -
624A ALA* 3.3 2.9 + - - +
636A HIS* 5.1 2.6 + - - -
637A TYR 3.2 12.8 - - - -
638A LEU* 4.5 5.4 - - - -
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Residues in contact with ILE 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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609A PHE* 3.9 28.5 - - + -
610A ILE 3.7 6.5 - - - +
611A ILE* 4.3 17.7 - - + +
621A PHE 4.0 0.4 - - - -
622A GLY* 1.3 71.0 - - - +
624A ALA* 1.3 61.4 + - - +
625A TYR* 3.8 3.1 - - + -
635A LYS 3.7 2.1 - - - +
636A HIS* 3.3 2.8 - - - -
637A TYR* 2.8 45.7 + - + +
639A VAL* 5.1 4.7 - - + -
651A PHE* 4.7 7.9 - - + -
654A PHE* 3.9 13.7 - - + -
655A LEU* 3.7 18.6 - - + -
661A PHE* 3.5 50.0 - - + -
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Residues in contact with ALA 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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597A VAL* 3.2 34.5 - - + -
601A LEU* 3.1 14.9 - - + +
609A PHE* 3.1 3.4 - - - -
610A ILE* 2.9 31.2 + - + +
622A GLY 3.3 3.7 + - - +
623A ILE* 1.3 70.3 - - - +
625A TYR* 1.3 61.2 + - - +
634A ILE* 4.9 1.6 - - + -
635A LYS 3.7 5.4 - - - -
636A HIS* 3.5 22.2 - - + +
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Residues in contact with TYR 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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601A LEU* 4.5 2.0 - - - -
607A GLY 5.1 0.2 - - - -
608A THR 3.0 11.7 - - - +
609A PHE* 3.5 13.2 - - + -
623A ILE* 3.8 7.4 - - + -
624A ALA* 1.3 73.9 - - - +
626A ILE* 1.3 74.8 + - - +
627A GLY* 4.4 5.6 - - - -
634A ILE* 3.8 1.3 - - - -
635A LYS* 2.8 93.4 + - + +
636A HIS 4.9 1.0 + - - -
637A TYR* 3.8 25.9 - - + +
660A GLN* 3.9 31.8 + - + +
661A PHE* 3.4 27.8 - + + -
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Residues in contact with ILE 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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601A LEU* 3.4 19.7 - - + +
603A ASN* 4.7 2.0 - - - +
604A GLN* 3.2 53.2 - - + +
605A ASP 3.9 8.5 - - - +
606A PRO* 3.5 17.7 - - + -
607A GLY* 2.9 22.7 + - - -
608A THR* 2.8 14.8 + - - +
625A TYR* 1.3 82.8 - - - +
627A GLY* 1.3 67.0 + - - +
628A VAL* 5.7 0.3 - - - +
632A ALA* 4.0 16.6 - - + -
633A ARG 4.0 7.0 - - - +
634A ILE* 4.5 14.8 - - + -
660A GLN 4.6 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