Contacts of the strand formed by residues 87 - 93 (chain L) in PDB entry 3STJ
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 ALA 87 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31L VAL* 3.7 24.6 - - + +
32L GLU 3.7 4.7 - - - -
61L PHE* 4.4 1.0 - - - -
84L ILE 3.0 18.4 + - - +
85L ASN 3.5 0.6 - - - +
86L GLN* 1.3 78.3 - - - +
88L GLN* 1.3 60.9 + - - +
89L LYS 4.2 1.3 - - - +
90L ILE* 3.6 33.6 - - + +
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Residues in contact with GLN 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L GLU 2.7 9.7 + - - +
33L GLY* 3.7 21.7 - - - +
34L THR* 3.4 30.4 - - + +
86L GLN 4.2 2.9 - - - +
87L ALA* 1.3 76.4 - - - +
89L LYS* 1.3 67.8 + - + +
90L ILE* 5.5 1.1 - - - -
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Residues in contact with LYS 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ARG 3.9 0.4 - - - +
31L VAL* 3.4 4.3 - - - -
32L GLU* 2.9 56.2 + - + +
87L ALA* 4.2 1.2 - - - +
88L GLN* 1.3 84.5 - - + +
90L ILE* 1.3 64.3 + - - +
91L SER* 5.4 1.3 - - - +
101L ASP* 5.4 6.1 - - - +
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Residues in contact with ILE 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 4.0 13.7 - - + -
30L ARG 3.4 3.6 - - - +
31L VAL* 3.9 3.8 - - + -
84L ILE* 3.7 22.4 - - + +
87L ALA* 3.6 23.1 - - + +
88L GLN 5.5 0.7 - - - -
89L LYS* 1.3 77.7 - - - +
91L SER* 1.3 62.2 + - - +
92L ILE* 4.0 6.3 - - + -
101L ASP* 3.3 12.7 + - - +
102L ALA* 2.9 51.0 + - + +
103L LYS* 5.2 0.2 - - - -
104L LEU* 4.4 19.5 - - + +
116L LEU* 3.9 27.1 - - + -
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Residues in contact with SER 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L SER 3.8 0.2 - - - +
29L VAL* 3.6 0.3 - - - -
30L ARG* 2.8 58.8 + - - +
89L LYS 5.4 1.2 + - - -
90L ILE* 1.3 73.7 - - - +
92L ILE* 1.3 69.0 + - - +
99L GLU* 5.9 4.9 - - - -
100L PHE 3.3 12.8 - - - -
101L ASP* 5.0 5.4 - - - -
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Residues in contact with ILE 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL* 3.9 34.5 - - + -
28L SER 3.3 3.6 - - - +
29L VAL* 4.0 7.4 - - + -
77L VAL* 4.6 9.9 - - + -
90L ILE* 4.0 4.5 - - + -
91L SER* 1.3 80.9 - - - +
93L GLN* 1.3 60.7 + - - +
94L LEU* 4.0 12.8 - - + -
98L ARG 3.9 0.3 - - - +
99L GLU* 3.3 6.9 - - - +
100L PHE* 2.8 40.2 + - + +
102L ALA* 3.6 24.2 - - + -
116L LEU* 3.9 22.0 - - + -
118L ILE* 4.0 27.6 - - + -
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Residues in contact with GLN 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL* 3.6 4.0 - - - -
28L SER* 2.9 51.8 + - - +
92L ILE* 1.3 75.9 - - - +
94L LEU* 1.3 77.8 + - - +
97L GLY* 4.1 12.8 - - - +
98L ARG 3.4 8.7 - - - +
99L GLU* 3.3 28.4 - - + +
146L ASN* 5.8 0.6 + - - -
151L GLY* 6.0 3.8 - - - -
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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