Contacts of the strand formed by residues 639 - 644 (chain A) in PDB entry 1JSC
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 639 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A VAL 3.1 4.9 + - - +
571A LYS* 3.3 28.5 - - + -
572A ILE* 2.8 26.5 + - - +
614A LEU* 4.1 6.2 - - - +
615A LYS* 3.3 27.4 - - + +
617A LEU* 4.0 26.7 - - + -
632A PHE* 3.5 22.7 - - + +
635A THR* 4.1 15.3 - - + +
637A GLY 4.3 0.7 - - - +
638A PRO* 1.3 75.5 - - - +
640A LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 640 (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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553A PHE* 3.7 21.3 - - + -
560A LEU* 4.5 7.9 - - + -
572A ILE* 3.2 17.3 - - + +
574A ILE* 3.7 30.3 - - + -
605A PHE* 4.2 27.6 - - + +
606A ILE* 4.3 7.2 - - + -
608A LEU* 5.5 0.4 - - + -
609A ALA* 4.0 19.7 - - + -
614A LEU* 4.6 4.9 - - + +
615A LYS 2.9 7.7 + - - +
616A GLY* 3.4 0.9 - - - -
617A LEU* 2.7 32.7 + - - +
639A VAL* 1.3 76.4 - - - +
641A LEU* 1.3 69.9 + - - +
642A GLU* 3.8 4.5 - - + +
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Residues in contact with LEU 641 (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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572A ILE 2.8 8.7 + - - -
573A LEU* 3.4 13.4 - - + +
574A ILE 2.9 23.7 + - - -
617A LEU* 3.2 30.7 - - + +
619A VAL* 3.8 19.5 - - + -
628A LYS* 4.2 10.8 - - + +
629A LEU* 4.0 20.9 - - + +
632A PHE* 3.4 48.2 - - + -
640A LEU* 1.3 75.6 - - - +
642A GLU* 1.3 67.3 + - - +
643A VAL* 4.0 9.6 - - + -
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Residues in contact with GLU 642 (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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574A ILE* 3.5 14.4 - - + +
576A ASN* 2.7 38.4 + - + +
605A PHE* 3.6 18.3 - - + -
606A ILE* 3.8 12.9 - - + +
617A LEU 2.8 7.5 + - - -
618A ARG* 2.6 44.9 + - + -
619A VAL 2.9 25.3 + - - -
640A LEU* 3.8 7.3 - - + +
641A LEU* 1.3 75.4 - - - +
643A VAL* 1.3 66.7 + - - +
644A GLU* 4.4 9.0 - - - +
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Residues in contact with VAL 643 (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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471A ILE* 4.3 15.9 - - + -
476A VAL* 4.0 26.5 - - + -
573A LEU* 3.8 22.7 - - + -
574A ILE 3.0 10.0 + - - +
575A LEU* 3.9 8.7 - - + -
576A ASN 3.2 17.3 + - - -
619A VAL* 3.7 14.6 - - + -
625A LEU* 4.3 10.8 - - + -
641A LEU* 4.0 13.9 - - + -
642A GLU* 1.3 79.2 - - - +
644A GLU* 1.3 73.1 + - - +
645A VAL* 3.0 12.0 + - + +
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Residues in contact with GLU 644 (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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470A LYS* 3.5 26.7 + - - +
471A ILE* 4.0 15.1 + - - +
576A ASN* 3.7 11.0 - - + +
618A ARG* 3.8 9.5 + - - -
619A VAL 2.9 17.5 + - - +
620A LYS* 3.2 49.3 - - - +
642A GLU* 4.0 17.9 - - + +
643A VAL* 1.3 75.3 - - - +
645A VAL* 1.3 61.4 + - - +
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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