Contacts of the helix formed by residues 657 - 672 (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 GLY 657 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A ARG 3.7 0.6 - - - -
656A LYS* 1.3 78.6 - - - +
658A TYR* 1.3 62.7 + - - +
659A GLY 3.3 2.2 - - - -
660A ARG* 3.7 5.5 + - - +
661A PHE* 3.2 21.7 + - - +
766A PRO* 6.1 1.1 - - - +
767A VAL* 4.6 11.6 + - - +
900A ACO 2.9 21.0 + - - -
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Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ILE* 5.1 9.0 - - + -
618A LEU* 3.4 26.9 - - + +
620A GLN* 4.2 28.7 + - + +
629A VAL* 3.9 22.4 - - + -
649A ILE* 3.8 21.5 - - + -
653A TYR* 3.7 23.6 - + + -
656A LYS* 3.3 28.0 - - + -
657A GLY* 1.3 76.1 - - - +
659A GLY* 1.3 59.7 + - - +
661A PHE* 3.3 7.1 + - + +
662A LEU* 2.9 32.6 + - - +
767A VAL* 4.5 25.8 - - + +
900A ACO 3.5 3.5 + - - +
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Residues in contact with GLY 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ILE* 3.9 1.2 - - - +
649A ILE* 3.7 10.7 - - - +
658A TYR* 1.3 69.1 - - - +
660A ARG* 1.3 59.8 + - - +
662A LEU* 3.1 4.5 + - - +
663A ILE* 2.8 36.0 + - - +
690A SER* 5.8 1.1 - - - -
900A ACO 2.6 46.2 + - - -
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Residues in contact with ARG 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A GLY* 4.1 6.5 - - - +
658A TYR 3.5 0.2 - - - -
659A GLY* 1.3 70.9 - - - +
661A PHE* 1.3 56.6 + - - +
663A ILE* 3.0 8.3 + - - +
664A ASP* 2.5 43.1 + - + +
690A SER* 5.9 2.4 - - - +
694A TYR* 3.4 41.0 - - + +
697A SER* 3.6 29.6 + - - -
698A VAL* 4.6 11.7 - - - +
761A GLN* 5.2 11.9 - - - +
766A PRO* 3.9 28.0 - - - +
768A ASP* 5.6 7.7 + - - -
900A ACO 2.7 31.7 + - + +
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Residues in contact with PHE 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A TYR* 3.8 34.3 - + - -
576A ILE* 5.0 7.9 - - + -
578A VAL* 4.1 12.3 - - + -
618A LEU* 3.5 34.8 - - + -
657A GLY 3.2 17.2 + - - +
658A TYR* 3.4 12.6 - + + +
659A GLY 3.2 0.2 - - - -
660A ARG* 1.3 74.9 - - - +
662A LEU* 1.3 58.9 + - + +
664A ASP* 3.3 1.7 + - - -
665A PHE* 2.7 43.0 + + + +
767A VAL* 3.1 32.1 - - + +
768A ASP* 3.9 4.0 - - - -
769A VAL* 3.4 45.3 - - + +
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Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A VAL* 4.3 15.0 - - + -
616A TYR 4.6 4.5 - - - +
618A LEU* 3.9 26.0 - - + -
630A GLY 4.2 3.1 - - - -
631A TYR* 3.2 41.5 - - - +
632A PHE* 3.7 27.1 - - + +
647A ILE* 3.8 10.5 - - + -
649A ILE* 3.8 17.5 - - + -
658A TYR 2.9 14.2 + - - +
659A GLY 3.6 6.3 - - - +
661A PHE* 1.3 79.3 - - + +
663A ILE* 1.3 64.8 + - - +
665A PHE* 3.1 5.9 + - + +
666A SER* 2.8 23.9 + - - -
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Residues in contact with ILE 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL* 5.4 0.9 - - + -
647A ILE* 3.2 25.6 - - + -
659A GLY 2.8 24.3 + - - +
660A ARG* 3.2 11.0 - - - +
662A LEU* 1.3 70.2 - - - +
664A ASP* 1.3 67.0 + - - +
666A SER* 2.4 28.3 + - - +
667A TYR* 3.3 5.1 + - + -
690A SER* 5.1 16.2 - - - +
691A TYR* 3.1 52.0 - - + +
694A TYR* 3.5 38.4 - - + -
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Residues in contact with ASP 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ARG* 2.5 27.1 + - + +
661A PHE* 3.5 3.8 - - - +
663A ILE* 1.3 73.2 - - - +
665A PHE* 1.3 64.3 + - - +
667A TYR* 2.9 15.6 + - - +
668A LEU* 3.1 12.0 + - - +
671A LYS* 5.4 5.9 + - - -
694A TYR* 2.8 34.6 + - + +
768A ASP* 3.3 23.8 - - - +
769A VAL* 3.6 19.3 - - + +
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Residues in contact with PHE 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 3.4 23.8 - - + -
571A TYR* 3.8 19.5 - + + -
578A VAL* 3.2 37.7 - - + -
616A TYR* 4.1 8.3 - + + -
632A PHE* 4.0 14.4 - + + -
661A PHE* 2.7 34.9 + + + +
662A LEU* 3.3 13.5 - - + +
664A ASP* 1.3 70.4 - - - +
666A SER* 1.3 64.9 + - - +
667A TYR 3.1 0.7 + - - -
668A LEU* 3.1 11.9 + - + +
669A LEU* 3.0 39.1 + - + +
769A VAL* 3.8 13.3 - - + +
774A LEU* 3.9 19.7 - - + -
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Residues in contact with SER 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A PHE* 3.5 28.5 - - - -
634A LYS* 5.5 0.7 + - - -
643A ASN* 4.0 14.0 + - - +
644A VAL* 3.4 32.8 - - - +
662A LEU 2.8 9.0 + - - -
663A ILE* 2.4 32.2 + - - +
665A PHE* 1.3 72.4 - - - +
667A TYR* 1.3 61.3 + - - -
669A LEU* 3.4 7.1 - - - +
670A SER* 3.4 18.7 + - - -
691A TYR* 4.6 1.4 + - - -
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Residues in contact with TYR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ASN* 2.9 34.1 - - - -
644A VAL* 6.4 0.2 - - + -
663A ILE* 4.0 14.6 - - + -
664A ASP* 2.9 8.8 + - - +
666A SER* 1.3 79.4 + - - +
668A LEU* 1.3 55.1 + - - +
669A LEU 3.0 1.3 - - - -
670A SER* 2.9 3.4 + - - -
671A LYS* 2.3 41.7 + - + +
677A GLY 3.8 12.3 - - - -
678A SER* 4.4 2.8 + - - -
679A PRO* 4.2 5.5 - - - +
691A TYR* 3.8 10.4 - + - -
694A TYR* 3.1 45.8 - + - +
695A TRP* 2.8 32.6 + + - -
719A LEU 4.4 6.3 - - - +
720A THR* 3.6 32.3 - - + +
721A GLY* 4.5 8.1 - - - -
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A TYR* 6.1 0.9 - - + -
664A ASP* 3.1 9.1 + - - +
665A PHE* 3.1 14.0 + - + +
667A TYR* 1.3 76.0 - - - +
669A LEU* 1.3 65.3 + - - +
671A LYS* 3.2 28.1 - - + +
672A ARG* 3.1 43.1 + - + +
769A VAL* 4.3 16.2 - - + -
770A ASP 5.1 0.2 - - - -
771A PRO* 3.6 42.0 - - + -
774A LEU* 3.8 26.5 - - + -
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Residues in contact with LEU 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TYR* 3.4 39.9 - - + +
632A PHE* 4.1 13.2 - - + -
634A LYS* 3.6 20.6 - - + +
665A PHE* 3.0 32.9 + - + +
666A SER 3.4 9.6 - - - +
667A TYR 3.0 0.6 + - - -
668A LEU* 1.3 79.2 - - - +
670A SER* 1.3 63.3 + - - +
672A ARG 3.4 0.2 + - - -
673A GLU* 3.2 24.6 + - - +
774A LEU* 4.8 4.0 - - + -
776A TRP* 3.4 49.5 - - + +
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Residues in contact with SER 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LYS* 4.9 1.1 - - - +
643A ASN* 3.6 32.7 + - - -
666A SER 3.4 0.8 + - - -
667A TYR* 2.9 12.8 + - - -
669A LEU* 1.3 75.0 - - - +
671A LYS* 1.3 67.4 + - - +
673A GLU* 3.0 31.4 + - - +
674A GLY 3.1 4.5 + - - -
675A GLN 3.2 27.4 + - - +
676A ALA 4.4 0.2 + - - -
677A GLY 4.1 1.1 + - - -
720A THR* 3.2 18.9 - - - +
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Residues in contact with LYS 671 (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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664A ASP* 5.4 5.5 + - - -
667A TYR* 2.3 31.3 + - - +
668A LEU* 3.2 34.2 - - + +
670A SER* 1.3 67.0 + - - +
672A ARG* 1.3 58.6 + - - +
674A GLY* 2.8 22.3 + - - -
717A SER 4.5 6.3 - - - +
718A LYS 4.1 11.9 + - - -
719A LEU* 3.3 33.5 + - - +
720A THR* 3.1 18.2 - - - +
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Residues in contact with ARG 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A LEU* 3.1 38.4 + - + +
669A LEU 3.7 5.8 - - - +
671A LYS* 1.3 75.7 - - + +
673A GLU* 1.3 61.1 + - - +
674A GLY 3.2 0.4 - - - -
771A PRO* 3.6 22.8 + - - +
774A LEU* 3.9 30.1 + - - +
776A TRP* 3.6 43.3 + - + +
778A PRO* 3.0 22.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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