Contacts of the strand formed by residues 1004 - 1009 (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 TYR1004 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A ARG* 2.6 41.7 + - + +
654A ASP* 4.0 2.7 - - - -
655A THR* 3.7 3.1 - - - -
681A LEU* 3.8 2.4 - - - +
818A HIS* 3.0 49.0 + + + -
857A PRO* 3.3 29.6 - - + +
858A TRP* 3.9 21.8 - + + -
859A ALA* 3.4 23.5 - - + +
965A LEU 3.6 4.0 - - - +
966A MET* 3.7 21.3 - - + -
967A GLY 3.9 12.6 - - - -
968A MET* 3.4 16.8 - - - -
1002A GLY 3.0 24.0 - - - -
1003A THR* 1.3 87.8 - - - +
1005A GLN* 1.3 60.4 + - - +
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Residues in contact with GLN1005 (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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651A GLU* 3.5 22.3 + - - +
653A ARG* 3.1 29.8 + - - +
852A ASP* 4.9 2.3 - - - +
856A ILE* 5.9 0.7 - - - +
857A PRO* 3.7 8.9 - - - +
963A TRP 3.4 2.8 - - - +
964A TYR* 3.5 1.7 - - - -
965A LEU* 3.1 35.0 + - + +
986A TYR* 4.6 11.7 - - + +
987A LYS 5.1 2.8 + - - -
997A PHE* 4.0 31.9 - - + -
999A ILE* 4.9 2.7 - - + -
1003A THR* 5.4 5.3 - - + +
1004A TYR* 1.3 72.6 - - - +
1006A THR* 1.3 78.9 + - - +
1007A LEU* 3.8 16.0 + - + +
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Residues in contact with THR1006 (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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653A ARG* 4.9 0.8 - - - +
853A SER* 4.3 18.0 - - - -
855A CYS 2.5 29.6 + - - +
856A ILE* 3.4 17.1 - - - +
857A PRO* 3.7 3.0 - - - +
962A ASN* 3.4 27.6 - - - +
963A TRP 3.3 4.0 - - - +
964A TYR* 3.7 11.8 - - + -
986A TYR* 4.5 7.3 - - - +
1005A GLN* 1.3 86.9 + - - +
1007A LEU* 1.3 76.8 + - - +
1008A GLU* 4.4 4.0 + - + -
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Residues in contact with LEU1007 (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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961A VAL 3.6 0.5 - - - +
962A ASN* 3.7 0.9 - - - -
963A TRP* 2.7 52.8 + - + +
965A LEU* 3.3 36.1 - - + -
979A PHE* 4.1 7.2 - - + -
984A PHE* 3.6 59.2 - - + -
985A GLN 4.3 2.0 - - - -
986A TYR* 4.3 8.7 - - + -
997A PHE* 4.5 9.6 - - + -
1005A GLN* 3.8 16.8 - - + +
1006A THR* 1.3 85.6 - - - +
1008A GLU* 1.3 62.3 + - - +
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Residues in contact with GLU1008 (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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853A SER* 3.1 29.0 + - - +
894A LYS* 5.2 2.8 + - - -
960A GLU* 3.3 25.3 - - - +
961A VAL 4.1 2.0 - - - -
962A ASN* 3.9 16.4 + - - +
984A PHE* 3.5 1.3 - - - -
985A GLN* 2.8 45.6 + - + +
987A LYS 5.0 0.2 - - - +
989A ARG 4.7 1.9 - - - -
990A GLY* 4.2 21.0 + - - -
1006A THR* 4.2 4.9 - - + -
1007A LEU* 1.3 71.9 - - - +
1009A MET* 1.3 60.2 + - - +
1010A PHE* 4.2 14.9 + - + -
215D ASN* 4.1 12.0 + - - +
216D LEU* 4.7 9.6 - - - +
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Residues in contact with MET1009 (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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955A MET* 5.3 2.5 - - - +
959A ASP 3.9 1.2 - - - +
960A GLU* 4.1 2.6 + - - +
961A VAL* 3.2 26.7 + - + +
963A TRP* 3.6 30.7 - - + +
979A PHE* 3.7 39.5 - - + -
982A HIS* 3.9 19.3 - - + +
983A SER 3.2 33.4 - - - +
984A PHE* 4.1 6.7 - - + +
1007A LEU 3.7 0.6 + - - -
1008A GLU* 1.3 73.5 - - - +
1010A PHE* 1.3 66.2 + - - +
1011A PRO* 3.2 24.2 - - + +
1035A TYR* 4.3 13.0 - - - -
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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