Contacts of the strand formed by residues 620 - 626 (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 ARG 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A PRO* 4.5 7.3 - - - +
593A TYR* 4.4 7.7 + - - -
616A ARG* 3.7 2.2 - - - +
617A VAL* 2.8 66.5 + - + +
619A ASN* 1.3 85.4 + - - +
621A LYS* 1.3 62.2 + - - +
622A TYR* 3.0 45.6 - - - +
671A VAL* 3.9 22.6 + - - -
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Residues in contact with LYS 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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564A ASP* 3.3 33.2 + - + +
585A ILE* 6.2 1.4 - - - +
588A GLU* 3.2 39.9 + - - +
589A VAL 5.0 1.7 - - - +
590A ILE* 4.1 16.8 - - + +
591A PRO* 4.0 13.5 - - - +
614A ILE* 4.0 16.6 - - + -
615A VAL 3.1 18.2 - - - +
616A ARG* 4.0 16.2 - - + +
619A ASN 4.2 1.5 - - - +
620A ARG* 1.3 77.7 + - - +
622A TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 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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590A ILE* 3.7 6.7 - - - -
591A PRO* 3.5 17.5 - - + +
593A TYR* 4.4 13.7 - + + -
614A ILE* 4.2 1.9 - - - +
615A VAL* 3.0 51.4 + - + +
617A VAL* 3.9 18.6 - - + -
620A ARG* 3.0 43.7 - - - +
621A LYS* 1.3 77.5 - - - +
623A GLY* 1.3 68.5 + - - +
624A ILE* 3.8 16.2 - - + +
667A VAL* 2.5 34.1 + - - +
670A ILE* 4.0 12.2 - - + +
671A VAL 3.8 14.0 + - - -
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Residues in contact with GLY 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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583A ILE* 5.9 1.1 - - - -
590A ILE* 3.2 7.1 - - - +
591A PRO 2.9 13.9 + - - +
592A VAL* 4.2 8.3 - - - -
593A TYR* 3.2 21.3 + - - +
612A ALA* 5.5 2.5 - - - -
613A VAL 3.6 5.8 - - - -
614A ILE* 4.0 15.7 - - - -
622A TYR* 1.3 74.7 - - - +
624A ILE* 1.3 71.7 + - - +
625A VAL 4.2 0.2 - - - -
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Residues in contact with ILE 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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558A ILE* 5.1 14.4 - - + -
593A TYR* 3.4 11.9 - - + +
595A LEU* 4.0 28.3 - - + -
612A ALA* 3.5 3.0 - - - +
613A VAL* 2.9 37.8 + - + +
615A VAL* 3.9 20.0 - - + -
622A TYR* 3.8 28.0 - - + +
623A GLY* 1.3 80.0 - - - +
625A VAL* 1.3 68.2 + - - +
626A VAL* 3.6 11.3 + - + +
665A ILE* 5.3 8.5 - - + -
667A VAL* 5.2 2.0 - - + -
670A ILE* 4.8 12.3 - - + -
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Residues in contact with VAL 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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569A ILE* 4.4 3.8 - - + -
592A VAL* 3.9 27.8 - - + -
593A TYR 3.0 9.8 + - - +
594A ARG* 4.2 12.1 - - + -
595A LEU* 3.2 22.7 + - - +
596A TRP* 3.9 18.3 - - + -
610A MET* 3.9 37.5 - - + -
611A GLU 3.6 11.4 - - - +
612A ALA* 4.0 13.0 - - + -
624A ILE* 1.3 72.6 - - - +
626A VAL* 1.3 74.9 + - - +
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Residues in contact with VAL 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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549A VAL* 3.4 44.9 - - + -
550A LYS 3.8 5.2 - - - +
551A VAL* 5.0 0.4 - - - -
558A ILE* 5.6 0.9 - - + -
595A LEU* 4.1 15.9 - - + -
596A TRP* 4.0 8.4 - - - -
610A MET* 4.9 2.1 - - - +
611A GLU* 3.0 31.2 + - + +
613A VAL* 5.0 6.7 - - + -
624A ILE* 3.9 14.4 - - + +
625A VAL* 1.3 85.9 - - - +
627A ASP* 1.3 67.2 + - - +
628A ASP 4.0 6.3 - - - +
629A LEU* 4.4 10.8 - - + -
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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