Contacts of the strand formed by residues 956 - 965 (chain A) in PDB entry 4UI2
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 956 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928A THR* 2.7 30.3 + - - -
929A ASN* 4.9 6.2 + - - +
955A THR* 1.3 71.8 - - - +
957A TYR* 1.3 63.9 + - - +
958A GLU* 6.0 1.3 - - - +
977A HIS* 3.9 37.7 - - + -
978A GLY* 4.6 2.5 - - - +
979A ALA* 3.8 21.7 - - + +
245D ASP 2.9 17.1 + - - +
246D GLY* 3.9 20.1 - - - +
247D THR* 4.4 15.5 - - + -
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Residues in contact with TYR 957 (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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926A TRP* 4.5 6.7 - + - -
927A LYS* 3.5 25.8 - - - +
928A THR* 3.8 15.5 - - + +
950A GLY 5.1 0.3 + - - -
951A LEU* 3.7 45.6 - - + +
952A LYS* 3.0 37.6 + - - +
955A THR* 3.4 34.5 - - + -
956A LEU* 1.3 77.6 - - - +
958A GLU* 1.3 59.5 + - - +
959A PHE* 3.7 19.9 - + + -
977A HIS* 3.3 7.2 - - - +
978A GLY 2.8 36.5 + - - +
980A THR* 4.3 3.6 - - + -
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Residues in contact with GLU 958 (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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926A TRP* 3.3 22.5 - - - +
927A LYS* 2.9 46.6 + - + +
928A THR* 5.1 0.9 - - - -
929A ASN* 4.2 10.9 + - - +
936A TYR* 3.2 25.4 + - + +
956A LEU* 6.0 1.0 - - - +
957A TYR* 1.3 72.8 - - - +
959A PHE* 1.3 68.3 + - - +
960A SER* 5.7 0.4 - - - +
975A THR* 4.5 15.0 + - - +
976A ALA 3.5 5.4 - - - +
977A HIS* 3.6 25.2 + - + +
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Residues in contact with PHE 959 (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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891A VAL* 4.5 5.1 - - + +
893A ALA* 4.2 7.6 - - + -
901A ILE* 3.9 28.5 - - + -
903A ILE* 3.4 50.5 - - + -
924A VAL* 5.2 3.1 - - + -
925A ARG 3.5 4.3 - - - +
926A TRP* 3.4 31.2 - + + -
936A TYR* 6.3 0.2 - - - -
948A VAL* 4.0 15.0 - - + -
951A LEU* 4.7 3.1 - - + -
957A TYR* 3.7 32.1 - + + -
958A GLU* 1.3 76.5 - - - +
960A SER* 1.3 61.4 + - - +
974A MET 4.1 0.9 - - - +
975A THR* 3.2 5.7 - - - -
976A ALA* 2.7 46.0 + - + +
978A GLY 4.1 6.5 - - - -
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Residues in contact with SER 960 (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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891A VAL* 5.1 0.7 - - - -
924A VAL* 3.6 3.7 - - - +
925A ARG* 2.6 71.4 + - - +
936A TYR* 4.7 2.6 + - - -
958A GLU* 5.7 0.9 - - - +
959A PHE* 1.3 76.7 - - - +
961A VAL* 1.3 66.8 + - - +
972A TRP* 3.8 6.1 - - - -
973A SER* 3.4 26.2 - - - -
975A THR* 3.9 10.8 - - - +
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Residues in contact with VAL 961 (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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888A PRO* 3.5 17.3 - - + +
891A VAL* 4.1 19.5 - - + -
903A ILE* 4.6 1.6 - - + -
905A TRP* 3.8 52.3 - - + +
922A TYR* 4.1 7.0 - - + -
923A THR 3.4 14.4 - - - +
924A VAL* 4.4 8.7 - - + -
960A SER* 1.3 79.9 - - - +
962A MET* 1.3 68.2 + - - +
972A TRP* 3.4 5.8 - - - -
973A SER* 2.8 38.6 + - - +
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Residues in contact with MET 962 (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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888A PRO* 4.0 6.3 - - - -
922A TYR* 3.3 3.8 - - - -
923A THR* 2.7 63.6 + - + +
961A VAL* 1.3 75.7 - - - +
963A VAL* 1.3 56.9 + - - +
964A THR* 4.1 19.3 - - + -
969A SER* 4.7 4.5 - - - -
970A SER* 3.7 20.4 - - - +
971A THR 3.6 15.7 - - - +
972A TRP* 3.4 40.1 - - + -
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Residues in contact with VAL 963 (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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885A MET* 4.0 29.4 - - + -
886A MET 3.7 12.6 - - - +
888A PRO* 4.1 7.1 - - + +
907A ASP* 4.2 6.7 - - - +
920A ARG* 4.1 13.2 - - - -
921A TYR 3.4 11.0 - - - +
922A TYR* 3.8 26.0 - - + -
962A MET* 1.3 74.5 - - - +
964A THR* 1.3 79.0 + - - +
969A SER* 3.7 0.2 - - - -
970A SER* 2.8 46.6 + - - +
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Residues in contact with THR 964 (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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920A ARG* 3.3 4.7 - - - +
921A TYR* 2.7 82.2 + - + +
923A THR* 4.3 3.1 - - - +
962A MET* 4.1 17.7 - - + -
963A VAL* 1.3 83.1 - - - +
965A LYS* 1.3 60.6 + - - +
966A GLY 4.1 5.8 + - - -
968A ARG 3.3 9.9 - - - -
969A SER* 3.5 17.7 - - - -
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Residues in contact with LYS 965 (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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885A MET* 3.7 28.2 - - + -
918A ASP* 3.1 37.5 - - - +
919A SER 5.2 1.3 - - - -
920A ARG* 4.0 17.5 - - + +
964A THR* 1.3 73.0 - - - +
966A GLY* 1.3 60.8 + - - +
967A ARG 3.1 8.7 + - - -
968A ARG* 2.6 29.2 + - + +
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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