Contacts of the strand formed by residues 952 - 959 (chain A) in PDB entry 3E4Z
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 HIS 952 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771A LEU* 3.5 38.9 + - + +
772A PRO 3.3 24.2 - - - -
773A ASP* 2.9 22.8 + - - -
775A GLY 4.1 2.0 - - - -
794A TYR 3.4 1.2 - - - +
795A TYR* 3.4 3.8 - - - +
796A GLN* 2.8 60.0 + - + +
797A THR 3.6 18.1 + - - -
943A MET* 4.0 8.2 + - + -
950A ARG* 3.0 23.9 + - + -
951A ARG* 1.3 79.5 - - - +
953A LYS* 1.3 59.4 + - - +
1005A PHE* 6.0 2.2 - + - -
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Residues in contact with LYS 953 (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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771A LEU* 4.5 1.0 - - - +
775A GLY 3.2 13.0 + - - +
776A TRP* 3.3 41.2 - - + +
777A PHE* 3.0 25.1 + - - -
793A ILE* 3.8 13.0 - - + -
794A TYR 3.4 5.2 - - - +
795A TYR* 3.7 26.6 + - + -
860A GLU* 2.7 29.9 + - - -
864A GLU* 2.5 29.8 + - - +
951A ARG* 3.8 17.8 - - + +
952A HIS* 1.3 73.0 - - - +
954A VAL* 1.3 66.8 + - - +
955A SER* 3.7 5.8 - - - +
986A LEU* 4.2 5.9 - - - +
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Residues in contact with VAL 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A LEU* 4.1 23.3 - - + +
689A LEU* 4.4 11.9 - - + -
690A MET* 3.9 17.7 - - + -
771A LEU* 3.2 40.8 - - + -
777A PHE* 3.4 21.8 - - + +
792A GLU 3.8 1.0 - - - +
793A ILE* 3.7 1.6 - - - +
794A TYR* 2.9 37.4 + - + +
953A LYS* 1.3 76.3 - - - +
955A SER* 1.3 72.8 + - - +
992A ILE* 4.7 2.9 - - + -
998A PHE* 4.7 0.4 - - + -
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Residues in contact with SER 955 (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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776A TRP* 3.1 18.4 + - - -
777A PHE 2.9 7.7 + - - +
778A VAL* 3.5 3.6 - - - -
779A TYR 2.9 25.6 + - - +
792A GLU 3.4 7.2 - - - -
793A ILE* 4.1 4.7 - - - +
860A GLU* 2.4 31.1 + - - -
953A LYS* 3.7 6.1 - - - -
954A VAL* 1.3 78.6 + - - +
956A VAL* 1.3 64.2 + - - +
957A HIS* 3.6 13.9 - - - -
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Residues in contact with VAL 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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682A ALA* 3.7 34.4 - - + +
685A TYR* 3.7 30.3 - - + -
686A LEU* 3.9 30.7 - - + +
689A LEU* 4.2 15.0 - - + -
779A TYR* 3.4 10.1 - - + +
781A GLN 5.9 0.2 - - - +
790A GLY 3.8 0.3 - - - +
791A ILE* 3.3 11.1 - - - +
792A GLU* 2.9 31.8 + - + +
955A SER* 1.3 75.8 - - - +
957A HIS* 1.3 63.5 + - - +
958A VAL* 4.2 3.8 - - + -
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Residues in contact with HIS 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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776A TRP* 5.1 1.6 - - - -
778A VAL* 3.9 22.9 - - + +
779A TYR 2.8 12.2 + - - +
780A GLN* 3.3 21.3 - - + +
781A GLN 2.9 28.1 + - - +
790A GLY 3.9 2.7 - - - -
791A ILE* 3.7 8.1 - - + +
856A PRO* 3.4 29.8 - - + +
857A HIS* 4.2 9.2 + - + +
860A GLU* 3.1 43.0 - - + +
955A SER* 3.6 11.5 - - - -
956A VAL* 1.3 79.0 + - - +
958A VAL* 1.3 63.6 + - - +
959A LEU* 3.9 0.7 - - + -
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Residues in contact with VAL 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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678A PRO* 3.7 17.5 - - + +
681A HIS* 4.1 7.4 - - + +
682A ALA* 3.7 37.2 - - + +
685A TYR* 4.0 20.6 - - + -
781A GLN 3.4 3.6 - - - +
782A ARG 4.2 3.1 - - - -
783A ASN* 3.7 34.1 - - + +
789A SER* 3.2 9.4 + - - -
790A GLY 2.8 40.6 + - - +
856A PRO* 4.1 1.6 - - - +
956A VAL* 4.2 0.7 - - + -
957A HIS* 1.3 75.7 - - - +
959A LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 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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780A GLN* 3.7 40.4 - - + +
781A GLN 2.8 21.5 + - - +
782A ARG* 3.7 11.4 - - + -
783A ASN* 2.9 28.4 + - - +
788A ASN 4.1 1.3 - - - -
789A SER* 3.9 2.2 - - - -
855A PRO* 6.0 0.2 - - + -
856A PRO* 4.0 26.0 - - + -
957A HIS* 5.1 0.7 - - + -
958A VAL* 1.3 73.5 - - - +
960A ALA* 1.3 68.4 + - - +
963A MET* 4.1 27.4 - - + +
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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