Contacts of the strand formed by residues 862 - 869 (chain 3) in PDB entry 5Z58
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 TRP 862 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7863 ARG* 4.4 6.1 - - - -
8023 THR* 3.6 24.0 - - + -
8033 ASP 3.4 21.5 - - - -
8043 HIS* 3.2 46.9 - + + -
8063 ALA 2.7 18.0 - - - +
8073 TYR 4.2 0.2 + - - -
8083 THR* 4.2 2.3 + - - -
8593 ASN 4.8 0.2 + - - -
8603 GLY 3.1 27.5 + - - -
8613 GLN* 1.3 76.1 + - - +
8633 ALA* 1.3 61.3 + - - +
8843 GLN* 2.9 23.8 + - - +
8853 ASN* 3.4 31.4 + - - +
8863 GLU 4.6 0.9 - - - +
8873 ALA* 4.0 10.5 - - + -
8893 PHE* 4.8 6.1 - + - -
9133 LEU* 3.4 52.2 + - + +
9153 LEU* 5.3 10.5 - - + -
567 ALA 4.7 4.9 - - - -
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Residues in contact with ALA 863 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7833 TYR* 3.5 36.3 - - + -
8023 THR* 2.8 30.5 - - - +
8033 ASP 2.9 11.7 + - - +
8063 ALA* 3.6 20.9 - - + -
8083 THR* 4.3 11.7 - - - +
8623 TRP* 1.3 77.3 - - - +
8643 SER* 1.3 60.0 + - - +
8833 GLU 5.5 0.2 - - - -
8843 GLN 4.6 2.0 - - - -
8863 GLU 4.8 0.2 - - - -
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Residues in contact with SER 864 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7833 TYR* 4.5 0.4 - - - -
8013 GLU 3.0 9.9 + - - -
8023 THR* 4.2 4.7 - - - -
8083 THR* 5.4 3.5 + - - -
8633 ALA* 1.3 75.5 - - - +
8653 VAL* 1.3 70.5 + - - +
8663 ILE* 5.4 0.7 - - - +
8823 LEU* 3.6 37.2 + - - +
8833 GLU 5.0 4.8 + - - +
8863 GLU 3.1 27.5 + - - -
8873 ALA* 4.2 2.2 - - - -
8883 ALA* 3.6 23.7 + - - +
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Residues in contact with VAL 865 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7823 GLN* 4.2 8.5 - - - +
7833 TYR* 3.4 29.2 - - + -
7993 ILE 3.7 0.3 - - - +
8003 ILE* 3.6 2.9 - - - +
8013 GLU* 2.8 51.3 + - - +
8083 THR* 4.9 6.1 - - - +
8643 SER* 1.3 81.0 + - - +
8663 ILE* 1.3 79.4 + - - +
8673 ARG* 5.6 0.2 - - + -
8793 LEU* 3.5 24.0 - - + -
8803 VAL 3.1 15.7 - - - +
8813 GLN* 4.7 10.8 - - + -
8823 LEU* 5.3 0.7 - - - -
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Residues in contact with ILE 866 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7983 ILE* 3.8 22.9 - - + -
7993 ILE 3.2 11.4 - - - +
8003 ILE* 4.7 9.9 - - + -
8643 SER* 5.4 1.6 - - - +
8653 VAL* 1.3 79.6 - - - +
8673 ARG* 1.3 66.8 + - - +
8793 LEU* 3.3 10.7 - - - +
8803 VAL* 2.9 47.2 + - + -
8823 LEU* 3.8 27.1 - - + -
9053 VAL* 5.5 0.9 - - + -
9073 VAL* 3.6 32.8 - - + -
9283 TYR* 4.4 9.4 - - + -
9373 LEU* 4.5 16.2 - - + -
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Residues in contact with ARG 867 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7803 PRO 5.0 1.7 + - - -
7813 LEU* 3.2 23.3 - - - +
7823 GLN* 3.9 25.5 - - - +
7973 LEU 3.2 1.1 - - - +
7983 ILE* 3.1 11.6 - - - +
7993 ILE* 2.9 43.1 + - + +
8013 GLU* 3.7 20.9 + - - -
8653 VAL* 5.2 0.6 - - + +
8663 ILE* 1.3 80.0 - - - +
8683 VAL* 1.3 67.2 + - - +
8693 MET* 3.6 31.8 - - + +
8763 THR* 3.2 46.0 + - - +
8783 ASP 3.5 4.9 - - - +
8793 LEU* 3.6 24.2 - - + +
8803 VAL* 5.9 0.2 - - - -
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Residues in contact with VAL 868 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7963 ASN* 4.3 10.8 - - + -
7973 LEU 3.5 2.9 - - - -
7983 ILE* 3.6 19.5 - - + -
8673 ARG* 1.3 72.1 - - - +
8693 MET* 1.3 54.1 + - - +
8763 THR* 3.2 3.3 + - - -
8773 LEU* 2.3 60.9 + - + -
8783 ASP* 2.9 31.9 + - + +
8803 VAL* 5.9 0.2 - - + -
9343 GLY 4.4 11.2 - - - +
9353 GLU 4.6 5.6 - - - +
9363 LYS 5.7 0.4 - - - -
9373 LEU* 3.6 36.6 - - + +
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Residues in contact with MET 869 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4353 LEU* 3.9 20.0 - - + -
7793 PHE* 3.9 31.0 - - + -
7803 PRO 4.1 9.2 - - - +
7813 LEU* 4.0 14.6 - - + -
7963 ASN* 3.8 2.8 - - - +
7973 LEU* 2.9 40.1 + - + +
7993 ILE* 4.6 6.1 - - + -
8673 ARG* 3.6 30.7 - - - +
8683 VAL* 1.3 74.3 - - - +
8703 ASN* 1.3 74.7 + - - +
8713 PRO* 3.5 0.5 - - - +
8743 GLY 3.8 15.3 - - - +
8753 ASN 3.4 12.3 - - - +
8763 THR* 4.5 6.3 - - - -
8773 LEU* 3.8 3.6 - - - -
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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