Contacts of the strand formed by residues 76 - 80 (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 TYR 76 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ILE* 3.5 3.8 - - - +
70L ILE* 2.8 49.1 + - + +
71L ASN* 3.0 26.2 + - + -
74L LYS* 3.5 37.7 + - + +
75L GLY* 1.4 74.1 - - - +
77L VAL* 1.3 54.6 + - - +
105L ILE* 4.2 11.9 - - + +
115L LEU* 4.2 16.4 - - + -
116L LEU 3.3 11.0 - - - +
117L GLN* 3.6 34.5 + - + -
232L ILE* 3.8 42.3 + - + +
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Residues in contact with VAL 77 (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 19.1 - - + -
29L VAL* 4.7 0.9 - - + -
67L GLY* 3.9 4.5 - - - -
68L VAL 3.3 21.1 - - - +
69L ILE* 3.9 16.4 - - + -
75L GLY 4.0 0.9 - - - +
76L TYR* 1.3 76.5 - - - +
78L LEU* 1.3 65.4 + - - +
79L THR 4.0 0.5 + - - -
92L ILE* 4.6 4.7 - - + -
114L ALA 3.9 0.5 - - - +
115L LEU* 3.5 7.0 - - - +
116L LEU* 2.8 62.2 + - + +
118L ILE* 3.7 35.0 - - + -
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Residues in contact with LEU 78 (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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67L GLY* 3.2 5.4 - - - -
68L VAL* 2.8 37.8 + - + +
70L ILE* 3.6 35.1 - - + +
76L TYR 4.2 0.6 + - - -
77L VAL* 1.3 70.8 - - - +
79L THR* 1.3 60.0 + - - +
113L ILE* 3.8 34.3 - - + -
114L ALA 3.8 8.3 - - - +
115L LEU* 4.4 6.5 - - + +
188L GLY 3.6 3.5 - - - +
198L LEU* 4.8 4.9 - - + -
201L ILE* 4.1 20.9 - - + -
224L ALA* 3.9 30.7 - - + +
225L ARG* 4.8 0.4 - - - +
228L ALA* 4.2 13.9 - - + -
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Residues in contact with THR 79 (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* 4.3 3.5 - - + +
66L SER 2.5 26.1 + - - -
67L GLY* 4.1 2.9 - - - -
77L VAL* 5.0 0.4 - - - -
78L LEU* 1.3 76.5 - - - +
80L ASN* 1.3 76.0 + - - +
83L VAL* 4.0 10.6 - - - +
84L ILE* 3.8 12.8 - - + -
112L ASP 4.0 0.3 - - - +
113L ILE* 3.8 10.9 - - - +
114L ALA* 3.0 33.6 + - + +
116L LEU* 3.8 29.4 - - + -
188L GLY* 3.4 13.2 - - - -
201L ILE* 4.6 5.0 - - - +
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Residues in contact with ASN 80 (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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79L THR* 1.3 88.3 + - - +
81L ASN* 1.3 64.8 + - - +
82L HIS* 3.4 23.8 - - + +
83L VAL* 3.4 23.2 + - + +
84L ILE 3.6 3.5 + - - -
112L ASP* 2.9 22.3 + - - -
114L ALA* 3.8 5.3 - - - +
187L SER* 3.2 7.6 - - - -
188L GLY* 2.6 28.1 + - - -
201L ILE* 4.4 3.2 - - - +
202L ASN 3.0 8.6 - - - +
203L THR* 3.2 32.5 + - - +
219L ILE* 3.9 2.4 - - - +
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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