Contacts of the strand formed by residues 126 - 131 (chain A) in PDB entry 2ZLE
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ASP* 1.3 78.1 - - - +
127A THR* 1.3 61.6 + - - +
143A GLY 3.4 14.6 - - - +
144A ILE* 3.4 18.2 - - + -
145A VAL* 5.1 0.2 - - - +
171A ASN* 4.0 19.8 - - - +
172A LEU* 3.6 37.9 + - + -
177A ILE* 4.8 1.6 - - - +
794C MET* 4.7 4.9 - - + +
795C PRO* 3.3 44.1 + - + +
796C SER* 4.0 7.0 - - - -
797C LEU* 3.7 27.7 - - + +
934C SER* 5.2 4.3 - - - -
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 1.3 74.4 + - - +
128A VAL* 1.3 63.4 + - - +
142A SER* 3.5 3.8 - - - -
143A GLY 2.8 33.7 + - - +
144A ILE* 3.9 11.2 - - - +
145A VAL* 3.8 11.3 - - - +
156A THR* 3.0 27.8 + - - +
158A ALA* 3.5 14.6 - - + -
169A LEU* 3.4 20.4 - - + +
170A VAL 3.8 4.0 - - - -
172A LEU* 5.6 3.3 - - - +
177A ILE* 3.5 24.3 - - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.9 7.4 - - + -
8A MET* 3.2 17.7 - - + -
9A LEU* 4.3 11.9 - - + -
127A THR* 1.3 77.3 - - - +
129A ALA* 1.3 64.5 + - - +
130A ILE* 4.7 3.2 - - + +
140A VAL* 3.7 24.0 - - + -
141A THR 3.5 13.2 - - - +
142A SER* 4.7 6.5 - - - -
168A ALA 3.8 0.3 - - - +
169A LEU* 3.5 4.2 - - - +
170A VAL* 2.8 74.9 + - + +
171A ASN 4.1 2.0 - - - +
172A LEU* 5.5 3.4 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 1.3 71.4 - - - +
130A ILE* 1.3 66.5 + - - +
131A GLY 4.3 0.2 - - - -
139A THR 3.9 0.6 - - - +
140A VAL* 3.2 5.0 - - - +
141A THR* 2.8 41.8 + - + +
158A ALA* 3.6 25.9 - - + +
168A ALA 3.2 8.5 - - - +
169A LEU* 4.1 4.9 - - + +
180A ASN* 3.9 13.9 - - - +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.5 12.1 - - + -
12A VAL* 3.7 29.8 - - + -
13A MET* 4.0 28.3 - - + -
16A VAL* 4.0 29.4 - - + +
52A SER* 4.6 3.0 - - - -
128A VAL* 4.7 6.7 - - + +
129A ALA* 1.3 81.9 - - - +
131A GLY* 1.3 63.2 + - - +
138A GLU* 5.1 4.7 - - + +
139A THR 3.5 8.7 - - - +
140A VAL* 4.3 11.2 - - + -
166A GLY* 5.4 0.2 - - - -
167A GLY* 3.5 5.0 + - - -
168A ALA* 2.9 38.0 + - + +
170A VAL* 5.0 8.7 - - + -
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A SER* 3.5 14.1 - - - -
129A ALA 4.3 0.2 - - - -
130A ILE* 1.3 77.5 - - - +
132A ASN* 1.3 59.9 + - - -
133A PRO* 3.1 9.4 - - - +
138A GLU* 3.4 5.4 - - - -
139A THR 2.8 33.9 + - - +
166A GLY* 4.2 15.0 - - - -
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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