Contacts of the strand formed by residues 793 - 802 (chain A) in PDB entry 5ID6
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 GLN 793 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.9 44.8 + - + +
746A MSE 3.6 4.1 - - - -
747A ARG* 2.5 89.9 + - - +
788A ARG* 3.9 17.4 - - - +
791A GLU* 3.2 9.4 + - + +
792A ASP* 1.3 73.9 - - - +
794A TYR* 1.3 72.8 + - - +
795A GLU* 3.8 13.1 + - - +
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Residues in contact with TYR 794 (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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20A LYS* 3.5 5.2 - - - +
21A ALA* 2.7 57.7 + - + +
23A PRO* 4.0 14.8 - - + -
28A GLN* 3.0 28.7 + - - -
31A ILE* 3.8 14.1 - - + +
37A LEU* 4.0 11.1 - - + +
523A LEU* 3.7 29.4 - - + -
525A PHE* 5.2 0.9 - + - -
702A PHE* 3.7 31.0 - + - -
744A LEU* 4.2 6.3 - - + -
745A PHE 3.3 10.1 - - - +
746A MSE 3.3 28.4 - - + +
792A ASP* 5.4 2.5 - - + -
793A GLN* 1.3 79.4 - - - +
795A GLU* 1.3 56.9 + - - +
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Residues in contact with GLU 795 (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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18A ARG* 5.2 5.7 + - + +
19A PHE 3.2 11.7 - - - +
21A ALA 4.4 0.2 - - - +
520A LYS* 4.0 25.4 - - + +
743A GLU 3.8 1.4 - - - +
744A LEU* 3.2 5.9 - - - +
745A PHE* 2.9 51.6 + - + +
747A ARG* 4.3 25.8 + - + +
793A GLN* 3.8 11.6 + - - +
794A TYR* 1.3 75.5 - - - +
796A LEU* 1.3 59.5 + - - +
797A HIS* 2.6 31.0 + - + +
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Residues in contact with LEU 796 (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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17A LEU 3.6 1.2 - - - +
18A ARG* 3.5 1.7 - - - -
19A PHE* 2.7 39.3 + - + +
21A ALA* 4.5 9.6 - - + -
531A MSE 3.3 31.4 - - + -
534A TRP* 5.6 1.6 - - + -
555A LEU* 4.2 20.2 - - + -
704A ILE* 3.8 37.9 - - + -
743A GLU 3.6 12.3 - - - +
744A LEU* 4.3 7.9 - - + -
795A GLU* 1.3 72.3 - - - +
797A HIS* 1.3 64.0 + - - +
798A ILE* 3.6 24.9 + - + +
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Residues in contact with HIS 797 (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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16A THR* 3.7 13.5 + - - +
17A LEU 3.3 4.3 - - - -
18A ARG* 3.5 32.9 + - + +
520A LYS* 4.2 8.7 - - - -
741A GLY 4.7 0.2 - - - +
742A ALA* 3.3 9.5 - - - +
743A GLU* 3.0 39.5 + - - +
745A PHE* 3.7 26.3 - + + -
795A GLU* 2.6 32.8 + - + +
796A LEU* 1.3 82.0 - - - +
798A ILE* 1.3 62.4 + - - +
799A PRO* 3.4 2.7 - - + +
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Residues in contact with ILE 798 (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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16A THR* 3.3 2.5 + - - -
17A LEU* 2.6 55.6 + - + +
19A PHE* 4.9 6.7 - - + -
534A TRP* 5.2 4.9 - - + +
546A ILE* 6.5 0.9 - - + -
724A PHE* 4.4 18.2 - - + -
727A LEU* 3.9 13.7 - - + -
738A LEU* 3.5 31.2 - - + -
742A ALA* 4.9 6.3 - - + -
796A LEU* 3.6 35.2 - - + +
797A HIS* 1.3 78.1 - - - +
799A PRO* 1.3 63.1 - - + +
800A ILE* 3.7 18.4 + - + -
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Residues in contact with PRO 799 (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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15A LYS 3.5 7.2 - - - +
16A THR* 4.0 12.6 - - + +
738A LEU* 3.8 4.0 - - - +
739A SER* 3.1 35.0 + - - +
740A GLY 3.6 17.0 - - - +
741A GLY* 3.5 18.2 - - - +
742A ALA* 3.8 14.6 - - + +
797A HIS* 3.4 10.5 - - + +
798A ILE* 1.3 88.2 - - + +
800A ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 800 (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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14A SER* 3.4 9.4 - - - -
15A LYS* 2.7 50.1 + - + +
17A LEU* 4.1 21.5 - - + -
723A TYR* 4.1 22.7 - - + -
727A LEU* 4.2 11.4 - - + -
736A ILE* 3.6 23.3 - - + -
737A ARG 3.1 14.1 - - - +
738A LEU* 4.8 0.2 - - - -
739A SER* 3.7 5.7 + - - -
798A ILE* 3.7 22.7 - - + +
799A PRO* 1.3 80.6 - - - +
801A ALA* 1.3 60.2 + - - +
802A ILE* 4.2 16.8 - - + -
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Residues in contact with ALA 801 (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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12A SER* 6.4 0.4 - - - -
13A LEU 3.9 3.8 - - - -
14A SER* 4.6 4.0 - - - +
735A GLN* 4.1 0.7 - - - +
736A ILE* 3.4 4.9 - - - +
737A ARG* 2.8 46.5 + - + +
739A SER* 3.7 11.4 + - - +
800A ILE* 1.3 74.1 - - - +
802A ILE* 1.3 62.6 + - - +
803A ASN 4.2 0.2 + - - -
804A LYS* 4.4 26.6 + - + -
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Residues in contact with ILE 802 (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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12A SER* 3.0 2.4 - - - -
13A LEU* 2.7 56.5 + - + +
15A LYS* 4.2 23.1 - - + -
723A TYR* 4.5 11.9 - - + -
735A GLN 3.9 6.3 - - - +
736A ILE* 4.2 17.9 - - + -
800A ILE* 4.2 19.3 - - + -
801A ALA* 1.3 76.0 - - - +
803A ASN* 1.3 73.1 + - + +
804A LYS 3.2 2.9 + - - -
956A TYR* 3.8 52.3 - - + +
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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