Contacts of the strand formed by residues 949 - 955 (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 PRO 949 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8893 PHE* 4.2 10.9 + - - +
8903 SER* 4.3 10.4 + - - +
9083 GLY* 3.6 11.2 - - - -
9093 VAL 3.4 38.9 - - - +
9243 PHE 4.1 5.2 - - - +
9253 VAL* 4.5 6.5 - - + -
9453 VAL* 4.6 4.0 - - + -
9473 GLU 3.5 8.1 - - - +
9483 VAL* 1.3 94.6 - - + +
9503 ALA* 1.3 61.0 + - - +
9513 ALA 4.6 2.9 - - - +
9523 ILE* 4.8 2.9 - - + -
9613 ILE* 4.2 14.8 - - + -
9623 GLY 3.8 14.8 - - - +
9633 VAL* 3.8 4.7 - - + -
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Residues in contact with ALA 950 (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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13031 ILE* 5.6 9.2 - - + +
8893 PHE* 4.1 18.5 - - + +
8903 SER* 4.2 4.2 - - - -
9483 VAL* 3.5 3.7 + - - +
9493 PRO* 1.3 73.9 - - - +
9513 ALA* 1.3 63.1 + - - +
9623 GLY 3.8 5.1 + - - -
9633 VAL* 5.0 0.4 - - - +
9643 GLY 5.2 1.1 - - - +
9893 TYR* 3.3 24.5 - - + +
9903 ILE* 3.0 29.8 - - + +
9913 SER 3.4 11.4 - - - +
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Residues in contact with ALA 951 (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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7873 LYS* 5.9 4.3 - - - +
8903 SER* 3.8 8.4 - - - -
9493 PRO* 3.5 1.5 - - - +
9503 ALA* 1.3 80.1 + - - +
9523 ILE* 1.3 71.9 + - - +
9613 ILE* 4.1 1.6 - - - +
9623 GLY 3.7 24.6 + - - +
9903 ILE* 5.4 4.8 - - + +
9913 SER 3.8 1.1 - - - +
9923 GLY* 3.8 21.3 - - - -
9933 ILE* 3.6 24.5 - - + +
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Residues in contact with ILE 952 (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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7873 LYS* 4.8 8.3 + - - +
8903 SER* 3.3 25.7 - - - +
8913 VAL 4.6 3.5 - - - +
8923 ALA* 3.7 30.1 - - + +
9063 LEU* 4.2 18.2 - - + +
9073 VAL 4.4 0.9 - - - -
9083 GLY* 3.5 25.6 - - - +
9253 VAL* 5.1 2.9 - - + -
9493 PRO* 4.8 2.9 - - + -
9513 ALA* 1.3 82.6 - - - +
9533 ALA* 1.3 66.0 + - - +
9543 PRO* 4.7 0.2 - - - +
9593 VAL* 3.6 27.6 - - + -
9603 LEU 3.6 5.6 - - - +
9613 ILE* 3.7 24.0 - - + -
9933 ILE* 4.3 2.7 - - - +
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Residues in contact with ALA 953 (chain 3).
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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9523 ILE* 1.3 75.9 - - - +
9543 PRO* 1.3 62.7 - - + +
9593 VAL* 3.6 4.8 - - - -
9603 LEU* 2.6 43.8 + - - +
9933 ILE* 3.8 29.3 - - + +
9943 GLN* 5.2 0.2 - - - -
9953 THR* 3.9 24.9 - - + +
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Residues in contact with PRO 954 (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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8923 ALA* 4.6 14.1 - - + -
8933 VAL 5.2 2.7 - - - +
8943 CYS* 3.6 35.0 - - + -
9523 ILE 4.7 0.2 - - - +
9533 ALA* 1.3 85.5 - - + +
9553 PHE* 1.3 60.3 + - - +
9573 GLY* 6.1 1.6 - - - +
9583 ARG 3.4 8.3 - - - +
9593 VAL* 4.2 3.1 - - - -
9953 THR* 2.9 25.2 + - - +
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Residues in contact with PHE 955 (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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9533 ALA 3.8 0.8 + - - -
9543 PRO* 1.3 74.6 - - - +
9563 GLN* 1.3 104.6 + - + +
9573 GLY 3.4 0.9 - - - -
9583 ARG* 2.6 31.3 + - - +
9603 LEU* 3.6 32.7 - - + +
9693 VAL* 6.1 2.5 - - + -
9953 THR* 4.2 4.3 - - + -
9963 ILE 3.6 20.9 - - - -
9973 GLY* 3.6 9.2 - - - -
9983 HIS 3.1 28.7 - - - -
9993 ARG 3.9 3.4 - - - -
10003 VAL* 3.8 12.1 - - + -
10143 TYR* 3.6 37.7 - + + -
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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