Contacts of the strand formed by residues 615 - 624 (chain I) in PDB entry 5A31
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 LEU 615 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588I PHE* 3.9 26.5 - - + -
599I CYS* 4.2 7.9 - - + -
600I ILE 3.6 13.7 - - - +
601I LEU* 4.2 8.7 - - + -
613I ASN* 4.5 5.6 - - - -
614I GLY* 1.3 80.5 - - - +
616I ILE* 1.3 71.5 + - - +
683I TYR 5.5 0.3 - - - +
684I GLN* 5.5 0.2 - - - -
685I PHE* 4.2 29.3 + - + +
689I TYR* 4.8 5.5 + - + -
693I LEU* 3.4 38.4 - - + -
700I ILE* 4.0 30.3 - - + -
701I PRO* 3.5 18.7 - - - +
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Residues in contact with ILE 616 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599I CYS* 3.5 1.8 - - - -
600I ILE* 2.8 43.9 + - + +
613I ASN* 5.1 8.3 - - + -
615I LEU* 1.3 79.4 - - - +
617I ALA* 1.3 71.1 + - - +
674I VAL* 3.7 46.4 - - + +
675I TYR* 3.9 21.8 - - + +
683I TYR* 4.1 16.8 - - + +
700I ILE* 4.6 3.1 - - - -
701I PRO* 3.8 16.6 - - + +
703I ARG* 3.8 19.3 - - + +
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Residues in contact with ALA 617 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597I LYS* 4.0 13.2 - - + -
598I MET 3.2 11.9 - - - +
599I CYS* 4.0 10.3 - - - +
616I ILE* 1.3 76.8 - - - +
618I ILE* 1.3 76.4 + - - +
700I ILE* 3.7 21.5 - - + +
701I PRO 3.0 12.0 + - - +
702I THR* 3.7 13.5 - - - +
703I ARG 3.3 18.2 + - - -
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Residues in contact with ILE 618 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597I LYS* 3.7 16.0 - - - +
598I MET* 2.9 26.1 + - + +
600I ILE* 4.3 17.3 - - + -
616I ILE 5.1 0.4 - - - +
617I ALA* 1.3 94.9 - - - +
619I LYS* 1.3 66.7 + - - +
620I PHE* 3.5 42.1 - - + -
669I LEU* 4.4 7.2 - - + -
674I VAL* 4.1 24.5 - - + -
702I THR* 4.0 3.4 - - - -
703I ARG* 3.8 6.5 - - + +
705I MET* 3.5 37.2 - - + -
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Residues in contact with LYS 619 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597I LYS* 4.5 8.3 - - - +
618I ILE* 1.3 77.8 - - - +
620I PHE* 1.3 70.2 + - - +
621I GLY* 5.3 1.8 - - - -
702I THR* 3.5 19.0 - - + +
703I ARG 3.2 8.4 + - - +
704I THR* 3.1 36.7 + - - +
705I MET* 3.0 24.8 + - - +
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Residues in contact with PHE 620 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598I MET* 4.6 15.5 - - + -
618I ILE* 3.5 36.6 - - + -
619I LYS* 1.3 78.8 - - - +
621I GLY* 1.3 62.8 + - - +
622I SER 3.8 0.7 - - - -
623I PHE* 3.6 21.3 - + + -
634I SER 4.3 3.8 - - - +
636I TYR* 3.5 29.1 - - + +
638I CYS* 5.0 2.5 - - + -
651I VAL* 3.9 33.9 - - + -
653I LEU* 3.6 33.4 - - + -
667I VAL* 4.6 2.7 - - + -
669I LEU* 4.7 3.4 - - + -
705I MET 3.8 4.3 - - - -
707I PHE* 3.5 28.7 - + - -
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Residues in contact with GLY 621 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619I LYS* 3.6 6.3 + - - -
620I PHE* 1.3 74.5 - - - +
622I SER* 1.3 60.1 + - - +
623I PHE* 5.1 1.3 - - - -
632I ARG 4.0 0.2 - - - +
633I ARG* 3.7 26.5 - - - +
634I SER 4.3 4.3 + - - +
636I TYR* 4.8 0.4 - - - -
704I THR* 4.1 18.2 - - - -
705I MET 2.9 17.4 + - - +
706I HIS* 4.6 5.4 - - - -
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Residues in contact with SER 622 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620I PHE 3.8 1.0 - - - -
621I GLY* 1.3 79.7 - - - +
623I PHE* 1.3 64.7 + - - +
624I THR* 5.5 2.4 - - - +
631I VAL* 3.8 22.0 - - - -
632I ARG 3.3 5.8 - - - -
633I ARG* 4.2 15.3 - - - -
705I MET 3.9 2.2 + - - -
706I HIS* 3.2 29.8 + - - +
707I PHE* 2.7 36.7 + - - +
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Residues in contact with PHE 623 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620I PHE* 3.6 31.9 - + + -
622I SER* 1.3 78.5 - - - +
624I THR* 1.3 60.6 + - - +
631I VAL* 4.5 0.4 - - - -
632I ARG* 2.5 52.1 + - + +
636I TYR* 3.7 33.4 - + - -
653I LEU* 3.5 22.4 - - + -
665I LEU* 3.9 11.4 - - + -
667I VAL* 3.5 31.2 - - + -
707I PHE* 3.3 24.2 - + + -
711I TRP* 3.6 35.4 - + + -
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Residues in contact with THR 624 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622I SER* 5.5 3.1 - - - +
623I PHE* 1.3 76.2 - - - +
625I TYR* 1.3 73.1 + - - +
628I THR* 3.9 0.2 + - - -
629I GLU* 4.8 1.7 + - - -
630I LYS 3.2 23.3 + - - -
631I VAL* 4.1 16.2 - - + +
632I ARG* 5.7 0.2 - - - -
707I PHE 3.0 9.3 + - - +
708I GLU* 2.7 41.9 - - + +
711I TRP* 2.7 27.1 + - - -
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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