Contacts of the strand formed by residues 903 - 911 (chain A) in PDB entry 4UHX
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 LEU 903 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A LEU* 3.5 7.9 - - + +
724A GLU* 3.5 3.3 - - - -
725A TYR* 2.8 41.3 + - + +
728A VAL* 4.6 4.2 - - - +
868A LEU* 3.4 41.1 - - + +
870A MET* 4.9 1.6 - - + -
894A MET* 3.6 30.7 - - + -
900A PHE* 3.8 20.2 - - + +
902A ASN* 1.3 74.6 - - - +
904A ARG* 1.3 65.9 + - - +
905A CYS* 4.0 10.5 - - + +
963A PRO* 3.5 35.7 - - + -
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Residues in contact with ARG 904 (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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722A LYS* 5.3 1.1 - - + -
723A LEU 3.5 4.3 - - - +
724A GLU* 3.1 26.7 - - - +
728A VAL* 3.9 26.1 - - + +
729A ASP* 5.1 9.4 + - - -
868A LEU 3.0 10.9 + - - +
869A ASP* 2.9 41.2 + - - +
870A MET 2.8 27.0 + - - +
903A LEU* 1.3 74.1 - - - +
905A CYS* 1.3 58.6 + - - +
906A ARG* 3.4 50.0 - - + +
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Residues in contact with CYS 905 (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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722A LYS* 3.4 5.0 - - - -
723A LEU* 2.9 51.0 + - + -
870A MET* 3.5 18.2 - - + -
872A HIS* 4.1 1.8 - - - -
891A LEU* 3.6 29.6 - - + +
894A MET* 3.3 40.8 - - - -
903A LEU* 4.5 6.7 - - + -
904A ARG* 1.3 72.9 - - - +
906A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 906 (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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720A GLU* 3.1 23.3 + - - +
721A ARG 3.5 7.6 - - - +
722A LYS* 3.8 22.4 - - + +
869A ASP* 5.2 0.8 + - - +
870A MET 3.0 12.8 + - - +
871A GLU* 3.3 20.0 + - + +
872A HIS* 2.8 32.6 + - - +
891A LEU* 4.1 5.6 - - - +
904A ARG* 3.4 37.8 - - + +
905A CYS* 1.3 81.1 - - - +
907A GLY* 1.3 52.6 + - - +
908A TRP* 3.6 36.8 - - + -
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Residues in contact with GLY 907 (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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719A PRO 4.5 1.6 - - - +
720A GLU* 4.4 0.2 - - - -
721A ARG* 3.2 24.0 + - - +
872A HIS* 3.4 11.2 - - - -
884A LEU* 5.5 0.3 - - - +
887A ILE* 3.7 24.8 - - - +
891A LEU* 4.1 5.7 - - - +
906A ARG* 1.3 75.7 - - - +
908A TRP* 1.3 74.5 + - - -
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Residues in contact with TRP 908 (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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718A LYS* 4.4 29.4 + - + +
719A PRO 4.1 16.2 - - - -
720A GLU* 3.5 38.9 - - + +
871A GLU* 4.1 15.7 - - + -
872A HIS 3.2 9.1 + - - -
873A TYR* 3.4 52.5 - + + -
874A SER 3.3 18.7 + - - -
884A LEU* 5.6 0.9 - - - -
887A ILE* 4.1 9.0 - - - +
906A ARG* 3.6 39.0 - - + -
907A GLY* 1.3 81.1 - - - -
909A ALA* 1.3 62.2 + - - +
910A CYS* 3.7 4.8 - - - -
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Residues in contact with ALA 909 (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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718A LYS* 3.7 23.9 - - - +
874A SER* 3.4 19.1 - - - +
876A ALA* 4.6 3.6 - - + -
880A LEU* 5.2 8.1 - - + -
883A SER* 3.7 29.6 - - - +
884A LEU* 4.6 13.1 - - + +
887A ILE* 4.1 5.6 - - + +
908A TRP* 1.3 73.5 - - - +
910A CYS* 1.3 58.6 + - - +
911A ARG 4.2 1.1 + - - -
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Residues in contact with CYS 910 (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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707A ILE* 4.0 29.6 - - + -
710A SER* 3.5 18.6 - - - +
711A ILE* 4.7 2.2 - - - -
718A LYS* 4.0 16.6 - - - +
873A TYR* 4.1 13.5 - - - -
874A SER 2.8 18.0 + - - +
875A ASN* 3.7 4.6 - - - -
876A ALA* 2.8 29.4 + - - +
908A TRP* 3.7 13.2 - - - -
909A ALA* 1.3 78.2 - - - +
911A ARG* 1.3 62.6 + - - +
912A THR* 3.5 3.4 + - + +
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Residues in contact with ARG 911 (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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669A PHE* 3.6 36.5 - - - +
704A ILE* 3.8 12.2 - - - +
710A SER* 2.8 26.8 + - - +
718A LYS* 5.3 2.8 - - - +
876A ALA* 4.4 3.3 - - + +
877A GLY 3.5 13.7 - - - +
878A ALA 3.3 23.6 + - - +
879A SER* 5.0 3.1 - - - +
909A ALA 4.2 1.6 + - - -
910A CYS* 1.3 69.6 - - - +
912A THR* 1.3 66.2 + - - +
913A ASN* 4.0 21.2 - - - +
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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