Contacts of the strand formed by residues 609 - 617 (chain A) in PDB entry 4JPB
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 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A SER* 3.7 36.0 + - - +
569A ILE 3.6 1.8 - - - -
570A SER* 3.1 29.2 + - - -
607A LEU* 3.5 24.0 - - - +
608A GLU* 1.3 82.8 - - - +
610A MET* 1.3 60.7 + - - +
131B ARG* 4.7 11.6 + - - +
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Residues in contact with MET 610 (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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568A SER* 3.5 4.4 - - - -
569A ILE* 2.8 49.4 + - + +
571A LYS* 3.6 31.0 - - + +
574A ILE* 4.5 14.6 - - - -
594A ARG* 4.8 0.9 - - - +
596A TRP* 6.1 0.2 - - + -
606A GLU* 3.6 25.4 - - - +
607A LEU* 3.2 30.1 - - + +
609A GLU* 1.3 75.3 - - - +
611A GLU* 1.3 63.7 + - - +
625A VAL* 3.9 37.9 - - + -
626A VAL 4.9 2.7 - - - +
131B ARG* 5.0 0.7 - - - +
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Residues in contact with GLU 611 (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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567A LEU 3.8 4.3 - - - +
610A MET* 1.3 74.3 - - - +
612A ALA* 1.3 60.1 + - - +
625A VAL* 3.6 2.1 - - - +
626A VAL* 3.0 36.9 + - + +
627A ASP 4.2 9.8 + - - +
628A ASP* 4.2 2.1 - - - -
629A LEU* 3.4 47.8 + - + +
131B ARG* 3.2 44.1 + - - +
134B ASN* 6.0 0.8 + - - -
135B ILE* 3.9 16.5 - - + +
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Residues in contact with ALA 612 (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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566A ILE* 3.8 3.7 - - - -
567A LEU* 3.0 52.2 + - + +
569A ILE* 3.9 22.2 - - + -
583A ILE* 5.7 0.2 - - + -
592A VAL* 6.2 0.4 - - + -
610A MET 3.9 0.2 + - - -
611A GLU* 1.3 75.7 - - - +
613A VAL* 1.3 62.1 + - - +
614A ILE* 3.6 0.9 + - + -
623A GLY* 5.4 3.4 - - - -
624A ILE 3.5 14.8 - - - +
625A VAL* 4.0 10.5 - - + -
629A LEU* 4.8 1.0 - - - +
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Residues in contact with VAL 613 (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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547A LEU* 3.6 26.0 - - + -
549A VAL* 4.7 6.5 - - + -
558A ILE* 4.0 19.7 - - + -
563A ILE* 4.0 22.0 - - + -
565A THR 4.0 4.0 - - - -
566A ILE* 4.6 6.1 - - + +
612A ALA* 1.3 71.6 - - - +
614A ILE* 1.3 65.0 + - - +
615A VAL* 3.7 24.1 + - + -
623A GLY 3.6 0.7 - - - -
624A ILE* 2.9 39.3 + - + +
626A VAL* 5.0 2.9 - - + -
629A LEU* 4.6 10.8 - - + -
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Residues in contact with ILE 614 (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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563A ILE* 3.6 4.9 - - - +
564A ASP* 2.8 31.5 + - + +
565A THR* 3.1 34.0 + - + +
567A LEU* 4.0 34.5 - - + -
583A ILE* 4.7 6.1 - - + -
585A ILE* 5.7 2.2 - - + -
590A ILE* 4.0 26.2 - - + -
612A ALA* 3.6 0.6 + - + -
613A VAL* 1.3 72.4 - - - +
615A VAL* 1.3 68.9 + - - +
621A LYS* 4.0 24.0 - - + -
622A TYR 3.8 10.5 - - - +
623A GLY* 4.0 9.0 - - - -
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Residues in contact with VAL 615 (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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558A ILE* 4.1 18.2 - - + -
562A ASN 3.3 13.5 - - - +
563A ILE* 4.5 0.4 - - - -
564A ASP* 4.8 1.1 - - - -
613A VAL* 3.7 20.6 + - + -
614A ILE* 1.3 78.5 - - - +
616A ARG* 1.3 62.7 + - - +
621A LYS* 3.1 8.2 - - - +
622A TYR* 3.0 57.7 + - + +
624A ILE* 3.9 12.3 - - + -
667A VAL* 3.4 31.0 - - + -
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Residues in contact with ARG 616 (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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561A ALA 3.6 22.8 + - - -
562A ASN* 3.0 26.7 + - - +
563A ILE 3.8 8.8 + - - -
564A ASP* 3.1 45.6 + - + +
615A VAL* 1.3 80.2 - - - +
617A VAL* 1.3 65.6 + - - +
618A GLY 3.5 22.3 + - - +
619A ASN* 5.3 1.6 - - - -
620A ARG 3.7 8.7 - - - +
621A LYS* 4.0 14.4 - - + +
146B ARG* 4.8 10.9 - - - +
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Residues in contact with VAL 617 (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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562A ASN* 6.0 0.2 - - - +
616A ARG* 1.3 77.2 - - - +
618A GLY* 1.3 63.7 + - - +
619A ASN* 3.0 5.4 + - - +
620A ARG* 2.8 60.7 + - + +
621A LYS* 4.6 0.2 - - - +
622A TYR* 3.9 5.8 - - + -
667A VAL* 3.6 42.8 - - + +
668A SER* 3.9 15.5 - - - +
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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