Contacts of the strand formed by residues 955 - 961 (chain A) in PDB entry 4B87
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 955 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865A ALA* 5.4 9.3 + - - +
868A LEU* 5.8 5.5 - - - +
869A ASN* 2.6 45.8 + - - +
871A HIS 4.0 0.9 + - - +
872A ALA* 4.0 13.6 - - + +
873A LEU* 2.7 32.0 + - - +
946A LEU* 4.0 5.3 - - - +
953A TYR 3.7 0.6 - - - -
954A ASN* 1.3 80.2 + - - +
956A ILE* 1.3 72.4 + - - +
957A LEU* 5.6 6.4 - - + +
983A ASN* 3.2 19.0 - - + +
985A SER* 5.6 5.2 + - - +
2043A EDO 3.7 16.6 + - - +
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Residues in contact with ILE 956 (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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873A LEU* 3.3 16.6 - - + +
875A VAL* 4.1 13.2 - - + -
942A LEU* 3.4 46.0 - - + +
945A HIS* 4.4 11.9 - - + -
946A LEU* 3.7 26.6 - - + +
955A GLN* 1.3 85.5 - - - +
957A LEU* 1.3 72.6 - - - +
958A ALA* 4.1 10.5 - - + +
983A ASN 2.9 9.0 + - - +
984A ILE* 3.4 14.1 - - + -
985A SER* 2.9 27.5 + - - -
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Residues in contact with LEU 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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861A THR* 4.1 9.4 - - + -
862A ALA* 5.0 2.0 - - - -
865A ALA* 3.4 31.4 - - + -
872A ALA* 5.6 3.8 - - + +
873A LEU 2.8 10.9 + - - +
874A VAL* 3.3 15.7 - - + +
875A VAL 2.8 24.4 + - - -
955A GLN* 4.2 9.1 - - - +
956A ILE* 1.3 74.6 - - - +
958A ALA* 1.4 57.0 + - - +
959A PHE* 3.2 42.4 - - + -
985A SER* 3.6 7.9 - - - +
987A TYR* 3.7 32.8 - - + +
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Residues in contact with ALA 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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875A VAL* 3.2 12.6 - - + +
937A ILE* 4.1 14.8 - - + -
942A LEU* 3.6 31.2 - - + -
956A ILE* 4.1 5.2 - - + -
957A LEU* 1.4 74.0 - - - +
959A PHE* 1.3 57.6 + - - +
985A SER 2.8 12.8 + - - +
986A ILE* 4.3 3.6 - - + -
987A TYR* 2.7 35.7 + - - +
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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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857A PHE* 4.6 2.0 - + - -
858A ALA* 3.7 31.9 - - + -
861A THR* 4.1 11.7 - - + -
862A ALA* 4.5 2.7 - - + -
874A VAL* 3.9 19.1 - - + -
875A VAL 2.9 10.4 + - - +
876A CYS* 3.8 17.9 - - - -
877A GLY 3.8 5.4 + - - -
886A VAL* 5.4 0.2 - - + -
890A ILE* 3.8 22.7 - - + -
937A ILE* 4.4 3.5 - - - +
957A LEU* 3.2 29.2 - - + -
958A ALA* 1.3 74.8 - - - +
960A ARG* 1.3 62.9 + - - +
987A TYR* 3.4 23.6 - + + -
989A ILE* 3.8 36.3 - - + -
2042A EDO 3.7 18.5 + - - +
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Residues in contact with ARG 960 (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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934A MET* 4.5 11.2 - - - -
937A ILE* 3.2 41.6 + - + -
938A ASN* 4.7 4.6 - - - +
959A PHE* 1.3 76.9 - - - +
961A PRO* 1.3 83.9 + - + +
963A GLY 5.7 2.7 - - - +
979A GLN* 3.3 28.9 + - - +
986A ILE* 3.6 28.1 + - + +
987A TYR 3.0 5.8 + - - +
988A GLY* 3.2 12.4 - - - +
989A ILE 2.9 22.5 + - - -
2042A EDO 3.5 6.1 - - - -
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Residues in contact with PRO 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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879A TYR* 5.9 2.7 - - + -
883A LYS* 4.3 18.8 - - - +
934A MET* 3.3 29.6 - - + -
960A ARG* 1.3 102.9 + - + +
962A THR* 1.3 69.2 + - - +
963A GLY 3.5 6.8 + - - +
988A GLY* 4.6 0.8 - - - -
989A ILE 3.2 10.3 - - - +
991A TYR 4.2 15.7 - - - +
2042A EDO 3.1 17.6 - - - +
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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