Contacts of the helix formed by residues 677 - 695 (chain A) in PDB entry 2RD0
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 ASN 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640A LYS* 5.8 2.2 + - - -
674A GLU* 3.5 19.3 - - + +
675A MET 3.2 0.8 - - - -
676A HIS* 1.3 91.0 - - + +
678A LYS* 1.3 52.7 + - - +
679A THR* 3.0 39.3 + - - +
680A VAL* 2.9 13.8 + - + +
681A SER* 2.8 29.0 + - - -
808A ARG* 5.7 2.8 + - - -
1009A GLY* 5.6 6.1 + - - -
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Residues in contact with LYS 678 (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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446A TRP* 4.7 8.1 - - + -
675A MET 5.7 0.2 - - - +
676A HIS 3.6 14.6 + - - +
677A ASN* 1.3 70.7 - - - +
679A THR* 1.3 61.2 + - - +
680A VAL 3.2 0.7 + - - -
681A SER* 2.7 20.5 + - - +
682A GLN* 4.8 2.9 + - - +
474B SER* 5.4 2.8 + - - -
475B GLN* 4.3 22.6 - - - +
478B GLN* 4.5 29.2 - - - +
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Residues in contact with THR 679 (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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446A TRP* 3.6 37.5 - - + -
461A VAL* 3.4 44.1 - - + +
677A ASN* 3.0 18.8 + - - +
678A LYS* 1.3 78.0 - - - +
680A VAL* 1.3 66.1 + - - +
683A ARG* 5.7 0.9 - - - +
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Residues in contact with VAL 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A VAL* 4.7 5.6 - - + -
640A LYS* 3.4 48.5 - - + +
674A GLU* 3.8 18.4 - - + +
677A ASN* 2.9 24.4 + - + +
679A THR* 1.3 88.9 - - - +
681A SER* 1.3 64.5 + - - +
682A GLN 3.2 2.9 + - - -
683A ARG* 3.2 13.5 + - + +
684A PHE* 2.9 38.7 + - + +
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Residues in contact with SER 681 (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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123A MET* 5.0 5.6 - - - -
675A MET* 3.4 35.2 + - - +
677A ASN 2.8 9.6 + - - -
678A LYS* 2.7 36.5 + - - +
680A VAL* 1.3 73.4 - - - +
682A GLN* 1.3 55.1 + - - +
684A PHE* 4.9 0.2 - - - -
685A GLY* 2.5 38.1 + - - -
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Residues in contact with GLN 682 (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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123A MET* 6.0 1.6 - - - -
128A PHE* 4.2 16.0 - - + -
131A VAL* 3.7 24.2 - - - +
133A ASP* 5.2 3.0 + - - +
136A VAL* 3.4 31.7 - - - +
645A LEU* 4.7 8.5 - - - +
678A LYS 4.8 3.2 + - - +
680A VAL 3.2 0.8 + - - -
681A SER* 1.3 75.2 - - - +
683A ARG* 1.3 67.6 + - - +
685A GLY 3.9 0.2 - - - -
686A LEU* 3.0 37.6 + - + +
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Residues in contact with ARG 683 (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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139A PHE* 5.9 0.3 - - - -
461A VAL* 6.1 1.8 - - - +
639A LEU* 3.1 27.4 + - + +
640A LYS* 2.8 32.3 + - - +
642A GLU* 3.7 16.1 - - - +
643A GLN* 3.8 7.7 + - - +
644A TYR 3.1 33.3 + - - -
645A LEU* 4.0 31.0 + - + +
647A ASN* 5.8 0.2 + - - -
679A THR 5.7 0.7 - - - +
680A VAL* 3.2 16.3 + - - +
682A GLN* 1.3 83.1 + - - +
684A PHE* 1.3 76.5 + - + +
686A LEU* 3.1 5.0 + - - +
687A LEU* 2.8 30.1 + - + +
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Residues in contact with PHE 684 (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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636A VAL* 4.0 25.8 - - + -
639A LEU* 4.3 15.0 - - + -
640A LYS* 4.3 20.0 - - + -
670A HIS 5.0 0.2 - - - -
671A LEU* 3.5 48.0 - - + +
674A GLU* 3.9 26.5 - - + +
675A MET* 3.9 14.6 - - - -
680A VAL* 2.9 26.9 + - + +
681A SER* 4.9 0.2 - - - -
683A ARG* 1.3 94.5 - - + +
685A GLY* 1.3 54.2 + - - +
687A LEU* 3.1 9.0 + - + +
688A LEU* 2.6 38.9 + - - +
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Residues in contact with GLY 685 (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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121A ILE* 3.8 6.7 - - - +
128A PHE* 3.5 19.2 - - - -
675A MET* 3.3 19.3 - - - -
681A SER 2.5 22.4 + - - -
684A PHE* 1.3 71.1 - - - +
686A LEU* 1.3 56.1 + - - +
688A LEU* 3.2 6.3 + - - +
689A GLU* 2.8 29.1 + - - +
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Residues in contact with LEU 686 (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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128A PHE* 3.6 29.5 - - + -
136A VAL* 3.8 21.5 - - + -
139A PHE* 4.0 26.5 - - + -
140A ARG* 3.5 30.1 - - + -
645A LEU* 4.0 21.3 - - + -
682A GLN* 3.0 34.5 + - + +
683A ARG* 3.2 4.0 - - - +
685A GLY* 1.3 73.1 - - - +
687A LEU* 1.3 68.2 + - - +
689A GLU* 3.3 6.4 + - - +
690A SER* 3.3 20.1 + - - -
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Residues in contact with LEU 687 (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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139A PHE* 4.4 10.1 - - + -
639A LEU* 3.8 23.1 - - + -
650A VAL* 3.7 33.7 - - + -
654A LEU* 3.9 17.7 - - + -
667A PHE* 3.7 33.2 - - + -
671A LEU* 4.0 15.0 - - + -
683A ARG* 2.8 15.4 + - + +
684A PHE* 3.3 13.7 - - + +
686A LEU* 1.3 76.7 - - - +
688A LEU* 1.3 60.7 + - - +
690A SER* 2.7 23.2 + - - +
691A TYR* 3.1 7.7 + - - +
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Residues in contact with LEU 688 (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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121A ILE* 3.9 19.1 - - + +
668A PHE* 3.5 49.4 - - + +
671A LEU* 3.6 21.1 - - + -
672A LYS* 3.6 33.0 - - + +
675A MET* 4.0 17.3 - - + -
684A PHE 2.6 20.9 + - - +
685A GLY* 3.5 5.6 - - - +
687A LEU* 1.3 71.9 - - - +
689A GLU* 1.3 57.6 + - - +
691A TYR* 3.1 9.7 + - + +
692A CYS* 2.8 33.1 + - - -
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Residues in contact with GLU 689 (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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117A ILE* 4.5 5.3 - - + +
121A ILE* 3.7 18.3 - - + +
125A VAL* 3.4 18.5 - - + +
128A PHE* 3.8 11.8 - - + -
140A ARG* 2.9 47.3 + - - +
685A GLY 2.8 14.7 + - - +
686A LEU* 3.3 8.0 + - - +
688A LEU* 1.3 68.6 - - - +
690A SER* 1.3 69.2 + - - +
692A CYS* 3.3 1.4 + - - +
693A ARG* 2.8 59.0 + - - +
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Residues in contact with SER 690 (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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139A PHE* 4.5 2.9 - - - -
143A ILE* 3.7 30.2 - - - +
144A LEU* 5.2 4.9 - - - -
147A CYS* 4.0 15.5 - - - -
654A LEU* 3.8 11.6 - - - +
686A LEU 3.3 9.2 + - - -
687A LEU* 2.7 27.0 + - - +
689A GLU* 1.3 80.5 + - - +
691A TYR* 1.3 63.7 + - - +
693A ARG* 3.1 14.8 + - - +
694A ALA* 3.4 13.3 + - - +
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Residues in contact with TYR 691 (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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165A TYR* 4.8 2.1 + - - -
654A LEU* 3.8 15.4 - - + +
657A ALA* 3.5 24.9 + - + -
658A LEU* 4.1 15.4 - - + +
661A GLN* 5.1 0.5 - - - +
664A GLY* 3.3 30.1 - - - -
667A PHE* 4.0 20.9 - + + -
668A PHE* 4.2 15.0 - + + -
687A LEU 3.6 8.1 - - - +
688A LEU* 3.1 12.9 + - + +
690A SER* 1.3 82.0 + - - +
692A CYS* 1.3 68.2 + - - +
694A ALA* 3.2 1.9 + - - -
695A CYS* 3.0 58.9 + - + +
698A TYR* 3.9 14.0 - - - -
702A LEU* 4.1 16.1 - - + +
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Residues in contact with CYS 692 (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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114A ASN* 5.5 0.5 - - - +
117A ILE* 3.6 29.1 - - + +
120A ALA* 4.3 7.2 - - - -
121A ILE* 4.6 8.1 - - - -
668A PHE* 4.3 21.3 - - - -
688A LEU* 2.8 25.3 + - - +
689A GLU 4.0 1.6 - - - +
691A TYR* 1.3 84.7 - - - +
693A ARG* 1.3 62.1 + - - +
694A ALA 3.1 1.9 + - - -
695A CYS* 3.6 19.1 + - - -
696A GLY 4.7 1.2 + - - -
699A LEU* 3.6 27.5 - - + +
702A LEU* 5.6 0.2 - - - -
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Residues in contact with ARG 693 (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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114A ASN* 4.2 23.5 + - - +
115A ARG* 3.7 36.7 - - - +
117A ILE* 3.7 16.7 - - + +
125A VAL* 3.3 21.4 - - - +
140A ARG* 4.7 1.0 - - - +
144A LEU* 4.9 16.4 - - + -
147A CYS* 6.1 0.4 - - - -
301A CYS 4.8 4.3 - - - +
302A PHE* 3.4 19.2 - - + -
303A THR 4.6 17.1 + - - +
304A MET* 5.2 4.0 - - - +
305A PRO* 4.2 10.3 - - - +
689A GLU* 2.8 53.5 + - - +
690A SER* 3.1 8.7 + - - +
692A CYS* 1.3 76.9 - - - +
694A ALA* 1.3 56.2 + - - +
696A GLY 5.5 0.4 - - - -
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Residues in contact with ALA 694 (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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147A CYS* 3.7 30.5 - - + -
151A VAL* 4.1 7.1 - - + +
154A ARG* 3.2 21.8 + - - -
301A CYS 5.4 3.1 - - - +
302A PHE* 3.8 13.0 - - + -
658A LEU* 3.4 17.5 - - + -
690A SER 3.4 6.9 + - - +
691A TYR 3.2 1.6 + - - -
692A CYS 3.1 0.2 - - - -
693A ARG* 1.3 80.3 - - - +
695A CYS* 1.3 64.8 + - - +
696A GLY* 3.2 4.4 + - - -
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Residues in contact with CYS 695 (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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154A ARG* 3.7 0.6 + - - -
165A TYR* 2.6 38.6 + - - +
299A MET* 4.1 1.0 - - - +
658A LEU* 3.5 5.8 - - - +
661A GLN* 4.1 4.0 - - - +
691A TYR* 3.0 48.5 + - + +
692A CYS* 3.6 20.4 - - - -
694A ALA* 1.3 76.2 - - - +
696A GLY* 1.3 60.8 + - - +
697A MET 4.1 0.3 + - - -
698A TYR* 4.2 6.0 + - + -
699A LEU* 3.7 29.8 - - - -
702A LEU* 5.0 1.6 - - - -
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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