Contacts of the strand formed by residues 617 - 631 (chain A) in PDB entry 5C58
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 GLU 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ARG* 2.9 19.0 + - - -
222A LEU* 3.3 25.0 - - + +
587A SER 3.9 0.2 - - - +
588A TRP* 3.4 8.8 - - - -
589A ARG* 2.8 69.0 + - + +
616A PRO* 1.3 71.8 - - - +
618A ARG* 1.3 60.1 + - - +
651A VAL* 4.0 12.6 - - + -
652A ASP 3.8 6.1 - - - +
653A ASN 3.4 16.4 - - - +
654A TYR* 3.4 11.2 - - - -
655A ILE* 2.6 30.4 + - + +
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Residues in contact with ARG 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LYS* 4.4 29.6 - - + +
586A LYS* 3.5 34.9 - - + +
587A SER 3.6 9.2 - - - +
588A TRP* 4.7 11.0 - - + +
616A PRO 3.7 3.8 + - - +
617A GLU* 1.3 74.3 - - - +
619A SER* 1.3 67.7 + - - +
620A ARG* 3.3 34.3 - - + +
650A LYS 4.1 0.2 - - - +
651A VAL* 3.6 2.9 - - - +
652A ASP* 2.9 47.2 + - - +
653A ASN* 5.1 2.5 - - - +
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Residues in contact with SER 619 (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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212A THR* 3.9 4.9 - - - +
222A LEU* 3.3 16.5 - - - +
586A LYS* 3.2 28.4 - - - +
587A SER* 2.2 38.5 + - - -
617A GLU 4.3 0.2 - - - -
618A ARG* 1.3 75.6 - - - +
620A ARG* 1.3 67.4 + - - +
621A ALA 4.2 0.4 - - - -
649A THR* 4.4 8.3 - - - -
650A LYS 3.3 5.2 - - - -
651A VAL* 3.7 19.3 - - - -
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Residues in contact with ARG 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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584A TYR* 3.7 32.0 + - + +
585A GLY 3.6 5.8 - - - -
586A LYS* 3.9 15.3 - - + +
618A ARG* 3.3 37.2 - - + +
619A SER* 1.3 80.3 - - - +
621A ALA* 1.3 59.8 + - - +
622A TRP* 4.8 5.9 - - + -
648A ASP 3.6 4.2 - - - +
649A THR* 4.7 0.2 - - - -
650A LYS* 2.9 52.7 + - + +
652A ASP* 5.9 1.1 + - - -
682A LYS* 5.4 8.1 - - - +
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Residues in contact with ALA 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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211A GLY* 5.5 1.8 - - - -
212A THR* 3.6 39.5 - - + +
583A THR 3.7 1.0 - - - +
584A TYR* 3.4 10.2 - - - -
585A GLY 3.0 27.1 + - - -
619A SER 4.2 0.2 - - - -
620A ARG* 1.3 73.6 - - - +
622A TRP* 1.3 64.4 + - - +
648A ASP 3.4 4.0 - - - -
649A THR* 3.9 19.5 - - + +
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Residues in contact with TRP 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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582A THR* 3.9 25.1 - - + -
583A THR 3.7 10.5 - - - -
584A TYR* 3.5 40.1 - + + -
620A ARG* 4.8 6.7 - - + +
621A ALA* 1.3 76.5 - - - +
623A GLU* 1.3 62.8 + - - +
624A VAL* 5.3 6.3 - - + -
646A TYR* 4.6 1.8 - - + -
647A PHE* 3.3 3.8 - - - +
648A ASP* 2.7 59.7 + - + +
649A THR* 5.4 0.2 + - - -
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Residues in contact with GLU 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.1 1.2 - - - +
122A SER* 2.8 37.6 + - - -
165A ARG* 4.0 13.1 + - - -
210A LYS 4.8 3.5 - - - +
211A GLY* 5.4 1.7 - - - -
581A TYR* 2.7 37.1 + - + +
582A THR* 3.3 7.0 - - - +
583A THR* 2.9 48.0 + - - +
622A TRP* 1.3 77.7 - - - +
624A VAL* 1.3 69.3 + - - +
645A ALA* 3.3 7.0 - - - +
646A TYR 3.2 12.3 - - - +
647A PHE* 4.5 3.8 - - + -
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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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581A TYR 3.6 7.9 - - - +
582A THR* 4.0 19.7 - - + +
622A TRP* 5.3 6.7 - - + -
623A GLU* 1.3 81.8 - - - +
625A GLY* 1.3 61.0 + - - +
645A ALA* 3.4 0.7 - - - -
646A TYR* 2.7 54.3 + - + +
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Residues in contact with GLY 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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580A LEU* 3.7 2.6 - - - +
581A TYR* 2.9 48.8 + - - +
624A VAL* 1.3 80.5 - - - +
626A PHE* 1.3 68.8 + - - +
644A VAL 3.2 13.7 - - - -
645A ALA* 4.0 0.7 - - - -
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Residues in contact with PHE 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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578A LEU* 3.5 26.7 - - + -
579A GLU 3.1 16.2 - - - +
580A LEU* 3.7 15.3 - - + -
581A TYR* 3.5 6.3 - - - -
625A GLY* 1.3 78.3 - - - +
627A ASN* 1.3 62.0 + - - +
628A VAL* 4.2 16.6 - - + -
642A ALA* 6.0 0.7 - - + -
643A LYS* 3.3 5.0 - - - +
644A VAL* 3.0 70.5 + - + +
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Residues in contact with ASN 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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117A TYR* 3.3 25.5 + - + +
119A GLU 3.2 27.3 + - - -
120A PRO* 4.9 0.2 - - - +
578A LEU* 3.8 3.9 - - - +
579A GLU* 3.2 47.9 + - - +
581A TYR* 4.3 10.9 - - - -
626A PHE* 1.3 76.2 - - - +
628A VAL* 1.3 64.4 + - - +
629A GLN* 4.2 0.6 + - - -
642A ALA 3.2 13.7 - - - +
643A LYS* 3.6 21.9 - - - +
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Residues in contact with VAL 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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117A TYR* 4.7 1.2 - - - +
577A TRP* 3.5 35.0 - - + +
578A LEU* 4.2 7.6 - - + -
626A PHE* 4.2 22.4 - - + -
627A ASN* 1.3 76.6 - - - +
629A GLN* 1.3 72.9 + - - +
630A GLN* 4.5 6.3 - - + +
640A LEU* 4.3 21.1 - - + -
641A VAL* 3.3 6.2 - - - +
642A ALA* 2.8 48.5 + - + +
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Residues in contact with GLN 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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114A ASP* 4.5 8.9 + - - -
117A TYR* 3.7 32.0 - - + +
118A ASP* 2.8 42.1 + - - +
572A ARG* 4.5 14.0 + - - +
576A GLU 3.8 17.7 - - - +
577A TRP* 3.4 8.2 + - - +
627A ASN 4.2 1.9 + - - -
628A VAL* 1.3 80.1 - - - +
630A GLN* 1.3 62.4 + - - +
631A PRO* 3.5 10.7 - - + +
640A LEU 3.7 4.3 - - - -
641A VAL* 4.3 9.4 - - + +
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Residues in contact with GLN 630 (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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577A TRP* 3.3 54.6 - - + +
628A VAL* 4.5 3.5 - - + +
629A GLN* 1.3 76.3 - - - +
631A PRO* 1.3 80.4 + - - +
632A ASP 3.8 2.5 + - - -
633A LEU* 4.1 16.5 + - + +
639A ARG* 3.8 1.6 - - - -
640A LEU* 3.0 43.5 + - + +
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Residues in contact with PRO 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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629A GLN 3.5 11.0 - - - +
630A GLN* 1.3 100.1 + - - +
632A ASP* 1.3 81.9 + - - +
638A ASP 4.1 8.1 - - - +
639A ARG* 4.5 4.7 - - + -
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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