Contacts of the strand formed by residues 585 - 592 (chain A) in PDB entry 3IJE
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 ASN 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A ALA* 5.9 0.2 - - - -
558A PHE* 3.4 23.4 - - + -
559A MET 2.9 19.7 - - - +
560A GLU* 3.6 4.5 + - + +
561A TYR* 3.7 6.5 - - - -
583A PRO* 3.2 18.4 + - - +
584A ALA* 1.3 82.1 + - - +
586A ILE* 1.3 61.6 + - - +
1G NAG 1.4 67.0 + - - +
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Residues in contact with ILE 586 (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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445A ALA* 3.9 23.8 - - + +
447A LEU* 3.7 22.6 - - + +
558A PHE* 3.8 3.3 - - - -
559A MET* 2.7 64.2 + - + +
585A ASN* 1.3 76.7 - - - +
587A SER* 1.3 69.0 + - - +
588A ARG* 3.2 31.9 - - - +
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Residues in contact with SER 587 (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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447A LEU* 4.2 1.8 - - - -
556A THR* 3.9 19.8 - - - +
557A ILE 3.5 2.7 - - - -
558A PHE* 3.6 22.2 - - - -
586A ILE* 1.3 76.7 - - - +
588A ARG* 1.3 76.6 + - - +
589A GLN* 6.0 1.6 - - - -
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Residues in contact with ARG 588 (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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446A GLY* 5.4 0.2 - - - -
447A LEU* 3.2 48.6 + - + +
448A GLU* 4.7 6.1 - - + +
449A VAL* 4.6 18.2 - - + +
556A THR* 3.3 5.8 - - - +
557A ILE* 2.7 38.5 + - + +
586A ILE* 3.2 32.3 - - - +
587A SER* 1.3 82.3 + - - +
589A GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 589 (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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449A VAL* 4.6 8.6 - - - +
452A SER* 4.4 8.1 + - - -
502A LEU* 5.3 0.6 - - - +
554A PRO* 3.7 9.2 - - + +
555A ILE 3.3 7.2 - - - +
556A THR* 3.2 31.4 + - - +
557A ILE* 4.1 2.0 - - - +
587A SER* 6.0 1.2 - - - -
588A ARG* 1.3 84.1 + - - +
590A ALA* 1.3 58.0 + - - +
591A HIS* 3.4 18.0 + - + -
640A GLU* 3.4 35.8 + - - +
685A ASN* 2.7 27.5 + - - +
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Residues in contact with ALA 590 (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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449A VAL* 4.7 11.4 - - + +
451A PRO 4.8 0.7 - - - +
452A SER 3.1 21.3 - - - +
454A LEU* 4.0 25.1 - - + -
473A PHE* 5.3 6.3 - - + -
554A PRO* 3.5 3.3 - - - +
555A ILE* 2.6 48.2 + - + +
557A ILE* 4.9 2.6 - - + +
589A GLN* 1.3 75.0 - - - +
591A HIS* 1.3 60.0 + - - +
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Residues in contact with HIS 591 (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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452A SER* 3.4 8.8 + - - -
453A ILE* 3.3 23.9 - - + +
454A LEU* 3.0 21.4 + - - -
552A LEU 5.6 2.5 + - - +
553A THR 5.3 0.9 - - - +
554A PRO* 3.5 23.9 - - + +
555A ILE 4.9 0.2 - - - +
589A GLN* 3.4 25.3 + - + -
590A ALA* 1.3 75.3 - - - +
592A ILE* 1.3 69.0 + - - +
639A TYR* 3.8 35.3 - + + +
640A GLU* 3.6 16.7 + - + -
685A ASN* 3.1 30.6 + - - -
686A PRO* 5.5 2.8 - - - +
720A SER* 4.4 1.9 + - - -
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Residues in contact with ILE 592 (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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453A ILE* 4.8 0.3 - - - +
454A LEU* 3.4 10.3 - - + +
456A GLN* 3.3 31.0 - - + +
510A ARG* 4.6 6.1 - - - +
542A LEU* 4.2 13.2 - - + -
548A PHE* 3.5 37.9 - - + -
550A ASP 4.3 1.1 - - - +
551A LYS* 4.0 35.0 + - + +
553A THR 5.2 3.9 + - - +
555A ILE* 4.2 25.6 - - + +
590A ALA 4.3 0.2 - - - -
591A HIS* 1.3 77.0 - - - +
593A LEU* 1.3 72.5 + - - +
594A LEU* 3.2 9.1 + - + +
639A TYR* 5.0 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