Contacts of the strand formed by residues 126 - 130 (chain B) in PDB entry 1ZMD
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 GLN 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.7 2.6 - - - +
122B THR* 2.7 59.0 + - - +
123B GLY* 2.6 16.8 + - - +
125B ASN* 1.3 82.2 - - - +
127B VAL* 1.3 74.0 + - - +
128B THR* 3.6 4.8 + - - -
138B VAL* 2.9 30.7 - - + +
139B ILE 3.3 12.8 - - - +
140B ASP* 3.4 17.3 - - - +
141B THR 4.7 0.2 - - - +
144B ILE* 4.1 1.2 - - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 4.0 19.1 - - + -
12B ILE* 4.2 12.1 - - + -
35B ILE* 3.6 23.1 - - + -
119B GLY* 4.4 1.1 - - - -
120B LYS 3.4 28.3 - - - +
121B ILE* 4.3 4.3 - - + -
122B THR* 4.0 0.2 - - - -
126B GLN* 1.3 81.4 - - - +
128B THR* 1.3 63.3 + - - +
129B ALA 4.0 0.2 + - - -
138B VAL 3.8 0.2 - - - -
139B ILE* 2.9 38.6 + - + +
141B THR* 4.6 2.5 - - + -
144B ILE* 3.8 35.9 - - + -
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR 3.6 3.1 - - - +
119B GLY* 3.6 1.6 - - - -
120B LYS* 2.9 31.2 + - - +
122B THR* 2.4 38.2 + - + +
126B GLN* 3.6 9.4 + - - -
127B VAL* 1.3 71.9 - - - +
129B ALA* 1.3 62.5 + - - +
130B THR* 3.7 15.9 + - - +
136B THR* 4.2 15.7 - - + -
137B GLN 3.4 11.4 - - - +
138B VAL* 4.2 11.1 - - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.2 22.4 - - + -
115B VAL* 3.5 32.3 - - + -
116B ASN 5.3 0.2 - - - +
117B GLY* 4.6 7.0 - - - -
118B TYR 3.7 5.8 - - - +
119B GLY* 4.2 1.3 - - - -
127B VAL 4.0 1.4 + - - -
128B THR* 1.3 70.3 - - - +
130B THR* 1.3 61.8 + - - +
131B LYS* 3.6 4.9 + - - -
135B GLY 4.1 0.2 - - - +
136B THR* 3.4 4.0 - - - -
137B GLN* 2.8 36.0 + - + +
139B ILE* 5.2 1.3 - - + +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TYR* 3.1 37.0 + - - +
120B LYS* 6.0 1.0 - - - +
128B THR* 4.2 10.4 + - - +
129B ALA* 1.3 69.6 - - - +
131B LYS* 1.3 77.5 + - - +
134B GLY* 3.8 13.7 - - - +
136B THR* 3.6 27.6 - - + +
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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