Contacts of the strand formed by residues 876 - 881 (chain A) in PDB entry 4EJX
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 876 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A LEU* 4.8 1.6 - - - -
790A GLY 4.2 1.6 - - - -
859A ALA* 3.6 0.2 - - - -
860A TYR* 2.8 56.7 + - - -
875A ILE* 1.3 81.6 - - - +
877A PRO* 1.3 67.7 - - - +
966A MET* 3.4 12.6 - - - +
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Residues in contact with PRO 877 (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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786A LEU* 5.5 3.6 - - + -
789A LEU* 4.3 12.6 - - + -
790A GLY 3.4 23.1 - - - +
791A PRO 3.7 0.9 - - - +
792A GLN* 3.7 13.0 - - + +
793A LEU 3.0 24.1 + - - +
857A PRO* 5.7 0.9 - - + -
858A TRP 3.7 4.0 - - - +
860A TYR* 3.3 9.7 - - + -
876A GLY* 1.3 82.8 - - - +
878A LEU* 1.3 60.4 + - - +
879A ILE* 4.6 11.9 - - + -
898A ALA* 4.1 26.0 - - + -
966A MET* 3.8 17.9 - - - -
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Residues in contact with LEU 878 (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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793A LEU* 3.4 25.1 - - + +
794A HIS 5.2 0.2 - - - -
795A ALA* 4.3 18.6 - - + -
801A VAL* 5.4 3.6 - - + -
817A ALA* 4.1 8.1 - - + -
820A VAL* 3.1 35.7 - - + -
840A TRP* 4.2 17.5 - - + -
842A ILE* 5.4 0.7 - - + -
856A ILE 3.8 0.3 - - - +
857A PRO* 3.2 5.0 - - - +
858A TRP* 2.7 65.5 + - + +
860A TYR* 3.7 12.4 - - + -
877A PRO* 1.3 72.5 - - - +
879A ILE* 1.3 61.1 + - - +
880A VAL* 3.8 8.6 + - + -
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Residues in contact with ILE 879 (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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792A GLN* 3.4 33.7 - - + +
793A LEU 2.5 17.1 + - - +
794A HIS* 3.4 21.4 + - + +
795A ALA 2.9 24.7 + - - +
855A CYS* 3.8 25.8 - - + -
856A ILE 3.6 5.2 - - - +
857A PRO* 3.8 13.5 - - + -
877A PRO* 4.6 8.3 - - + +
878A LEU* 1.3 81.4 - - - +
880A VAL* 1.3 61.6 + - - +
881A CYS* 3.5 1.7 + - - +
885A TYR* 6.0 0.2 - - - -
964A TYR* 3.7 43.3 - - + +
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Residues in contact with VAL 880 (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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795A ALA* 3.0 20.2 - - + +
797A VAL 4.7 0.4 - - - +
820A VAL* 4.9 0.4 - - + -
842A ILE* 3.8 23.3 - - + -
846A SER* 3.3 23.3 - - - +
847A GLY* 3.7 12.3 - - - -
848A ALA 4.6 0.7 + - - -
854A ALA 3.1 11.1 - - - +
855A CYS* 4.5 0.2 - - - -
856A ILE* 3.1 28.0 + - + +
858A TRP* 3.5 28.7 - - + +
878A LEU* 3.8 18.7 + - + -
879A ILE* 1.3 70.0 - - - +
881A CYS* 1.3 64.5 + - - +
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Residues in contact with CYS 881 (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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795A ALA 2.9 7.2 + - - +
796A ASP* 3.3 17.7 - - - +
797A VAL* 3.0 27.0 + - - +
848A ALA 5.5 0.7 - - - -
854A ALA* 3.0 13.5 - - - -
855A CYS* 2.0 55.6 - - - -
879A ILE 3.5 2.6 + - - +
880A VAL* 1.3 75.3 - - - +
882A ARG* 1.3 66.0 + - - +
885A TYR* 3.7 24.9 - - + -
217D HIS* 4.3 2.7 - - - -
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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