Contacts of the strand formed by residues 113 - 117 (chain L) in PDB entry 1ZA3
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 SER 113 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135H THR* 6.6 0.2 - - - -
111L ALA 3.7 2.8 + - - -
112L PRO* 1.3 70.1 - - - +
114L VAL* 1.3 60.2 + - - +
115L PHE* 3.6 20.7 - - - -
134L LEU 3.4 3.1 - - - +
136L ASN* 3.1 44.2 + - - +
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Residues in contact with VAL 114 (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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112L PRO* 3.5 14.6 + - + +
113L SER* 1.3 72.1 - - - +
115L PHE* 1.3 75.8 + - - +
133L CYS* 4.0 18.2 - - - -
134L LEU 3.3 5.6 - - - +
135L LEU* 4.4 5.2 - - + -
193L CYS* 4.3 2.2 - - - +
195L VAL* 3.6 42.8 - - + -
204L VAL* 4.1 19.7 - - + +
206L LYS* 3.5 40.9 - - + +
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Residues in contact with PHE 115 (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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127H SER 6.2 1.3 - - - -
135H THR* 4.5 21.1 - - + -
136H ALA* 4.3 7.2 - - - -
137H ALA* 3.5 47.3 - - + -
183H THR* 4.6 10.5 - - + -
113L SER* 3.6 30.1 - - - -
114L VAL* 1.3 84.3 - - - +
116L ILE* 1.3 61.5 + - - +
117L PHE* 4.5 7.6 - - + -
132L VAL 3.8 1.0 - - - +
133L CYS* 3.4 4.9 - - - -
134L LEU* 2.8 52.5 + - + +
136L ASN* 4.9 1.3 - - + -
206L LYS* 4.7 3.6 - - + -
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Residues in contact with ILE 116 (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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127H SER 4.4 10.5 - - - +
115L PHE* 1.3 75.5 - - - +
117L PHE* 1.3 78.3 + - - +
118L PRO* 4.0 5.1 - - + +
131L VAL* 4.3 3.6 - - + -
132L VAL 3.5 7.4 - - - +
133L CYS* 4.7 0.4 - - - +
147L TRP* 4.2 9.9 - - + -
191L TYR 3.8 14.4 - - - +
192L ALA* 3.8 9.6 - - - -
193L CYS* 4.0 11.0 - - - +
206L LYS* 3.2 44.4 - - + +
207L SER 4.1 4.7 - - - +
208L PHE* 3.7 39.0 - - + +
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Residues in contact with PHE 117 (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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124H LEU* 3.6 48.5 - - + -
125H ALA 3.4 26.0 - - - -
126H PRO* 4.9 0.2 - - + -
137H ALA* 3.6 31.9 - - + -
138H LEU* 4.0 9.9 - - - -
181H VAL* 4.5 4.0 - - + -
115L PHE* 4.5 7.6 - - + -
116L ILE* 1.3 80.7 - - - +
118L PRO* 1.3 69.2 - - + +
130L SER 4.5 0.7 - - - +
131L VAL* 3.4 9.5 - - - +
132L VAL* 2.9 57.9 + - + +
134L LEU* 4.0 27.6 - - + -
208L PHE* 3.9 3.1 - - - -
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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