Contacts of the strand formed by residues 613 - 622 (chain A) in PDB entry 2RC4
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 PHE 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A ASP* 4.1 0.9 - - - +
583A GLY* 3.0 28.8 + - - -
604A LYS* 6.1 2.2 - - - -
606A LEU* 4.3 23.3 - - + -
609A ASP 3.9 16.8 - - - -
610A VAL* 2.7 22.9 + - - +
611A GLU 3.8 2.1 - - - +
612A PRO* 1.3 86.1 - - + +
614A LEU* 1.3 65.9 + - - +
615A PHE* 3.6 19.6 - + + -
633A SER* 4.3 7.6 - - - +
634A LYS 3.4 10.3 - - - +
635A GLU* 3.4 38.8 - - + -
636A LYS* 4.3 0.2 - - - -
645A SER* 3.2 27.8 - - - -
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Residues in contact with LEU 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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580A GLU* 3.4 21.8 - - + +
581A VAL 3.6 7.9 - - - +
582A ASP* 4.1 11.2 - - + +
583A GLY 4.5 0.2 - - - +
613A PHE* 1.3 72.7 - - - +
615A PHE* 1.3 62.4 + - - +
616A TYR* 3.1 39.6 - - + +
633A SER* 3.9 2.6 - - - -
634A LYS* 2.8 33.1 + - + +
636A LYS* 3.4 41.7 - - + +
776A TRP* 6.0 0.9 - - + -
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Residues in contact with PHE 615 (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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579A PHE 3.3 1.7 - - - +
581A VAL* 2.5 50.2 + - + +
590A CYS* 3.3 36.6 - - + -
593A LEU* 3.6 29.6 - - + -
594A CYS* 3.7 21.8 - - - -
604A LYS* 5.1 1.6 - - - -
610A VAL* 3.8 31.2 - - + -
613A PHE* 3.6 28.9 - + + -
614A LEU* 1.3 74.8 - - - +
616A TYR* 1.3 59.8 + - - +
617A VAL* 3.7 2.0 + - + +
631A TYR* 4.0 8.3 - + - -
632A PHE 3.9 2.9 - - - +
633A SER* 3.5 21.8 - - - -
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Residues in contact with TYR 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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570A ILE* 3.6 24.7 - - + -
578A VAL* 5.3 5.2 - - + -
579A PHE 3.3 5.8 - - - +
580A GLU* 2.9 42.5 + - + -
614A LEU* 3.1 37.6 - - + +
615A PHE* 1.3 73.9 - - - +
617A VAL* 1.3 61.0 + - - +
618A LEU 3.9 0.9 + - - -
631A TYR* 3.1 3.2 - - - -
632A PHE* 3.0 63.0 + + + +
634A LYS* 4.1 19.0 + - + +
662A LEU* 4.6 3.1 - - + +
665A PHE* 4.1 6.1 - + + -
669A LEU* 3.4 34.0 - - + +
776A TRP* 4.2 3.8 + - - -
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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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565A PRO* 3.3 41.7 - - + -
577A SER 3.6 0.5 - - - +
578A VAL* 3.2 4.4 - - - -
579A PHE* 2.8 46.5 + - + +
581A VAL* 4.7 2.2 - - + -
589A TYR* 4.1 16.6 - - + +
593A LEU* 3.7 31.6 - - + -
615A PHE* 4.3 7.6 - - + +
616A TYR* 1.3 74.4 - - - +
618A LEU* 1.3 62.2 + - - +
619A THR* 4.6 1.8 - - + -
628A LEU* 5.0 6.7 - - + -
630A GLY 3.6 4.9 - - - +
631A TYR* 3.7 7.2 - - + -
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Residues in contact with LEU 618 (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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576A ILE* 4.3 17.5 - - + -
577A SER 3.2 16.8 - - - +
578A VAL* 3.8 4.3 - - + -
616A TYR 3.9 1.8 + - - -
617A VAL* 1.3 72.5 - - - +
619A THR* 1.3 63.5 + - - +
628A LEU* 3.9 1.2 - - - +
629A VAL* 2.9 36.6 + - + +
630A GLY 2.6 18.0 + - - +
649A ILE* 5.1 1.8 - - + -
658A TYR* 3.4 40.8 - - + +
661A PHE* 3.5 33.0 - - + -
662A LEU* 3.9 27.8 - - + -
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Residues in contact with THR 619 (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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565A PRO* 3.7 31.6 - - + -
576A ILE* 3.4 5.5 - - - +
577A SER* 2.7 37.5 + - - -
579A PHE* 3.3 21.9 - - + -
617A VAL* 4.4 2.7 - - + +
618A LEU* 1.3 79.0 - - - +
620A GLN* 1.3 57.9 + - - +
621A ASN* 2.8 22.5 + - - +
626A CYS* 3.6 14.4 - - - +
627A HIS 3.0 20.9 - - - +
628A LEU* 4.0 4.5 - - - +
629A VAL* 3.4 4.7 - - - -
658A TYR* 6.2 0.2 - - - -
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Residues in contact with GLN 620 (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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517A TYR* 5.4 0.3 + - - -
575A ASN* 3.9 15.1 - - + +
576A ILE* 4.8 1.3 - - - +
619A THR* 1.3 71.4 - - - +
621A ASN* 1.3 68.0 + - - +
622A ASP* 5.9 1.6 - - + +
627A HIS* 2.9 41.8 + - + +
629A VAL* 3.5 11.9 - - + +
653A TYR* 3.3 29.7 + - + -
658A TYR* 4.2 22.4 + - + +
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Residues in contact with ASN 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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569A GLU* 4.8 4.0 + - - -
575A ASN* 3.2 31.8 + - - +
577A SER* 3.1 18.2 + - - -
619A THR* 2.8 27.0 + - - +
620A GLN* 1.3 81.9 - - - +
622A ASP* 1.3 64.4 + - - +
625A GLY 3.3 7.0 - - - +
626A CYS* 3.0 34.1 - - - +
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Residues in contact with ASP 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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620A GLN* 5.9 1.4 - - - +
621A ASN* 1.3 76.5 - - - +
623A VAL* 1.3 66.8 + - + +
624A LYS* 2.7 34.6 + - - +
625A GLY* 2.9 19.6 + - - +
627A HIS* 2.9 31.1 + - - -
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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