Contacts of the strand formed by residues 124 - 130 (chain C) in PDB entry 1ZM9
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 GLY 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASN 3.1 8.5 + - - -
22C MET* 3.3 23.6 - - - +
23C SER 3.5 3.1 + - - -
122C THR* 3.7 5.0 + - - -
123C ASP* 1.3 79.3 - - - +
125C ALA* 1.3 65.2 + - - +
151C ILE* 3.3 8.2 - - - +
152C LYS 3.6 8.1 - - - -
342C LEU* 3.7 15.9 - - - -
343C PRO* 4.2 6.5 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C MET* 4.5 0.9 - - - -
23C SER* 3.6 7.9 - - - +
25C ILE* 3.3 33.0 - - + -
119C LEU* 5.7 0.4 - - + -
124C GLY* 1.3 76.1 - - - +
126C LEU* 1.3 55.4 + - - +
127C VAL* 3.6 2.2 + - + -
143C LEU* 6.2 0.4 - - + -
146C ALA* 5.2 1.1 - - + -
151C ILE* 3.6 14.8 - - + -
152C LYS 3.0 8.0 + - - +
153C PRO* 3.5 5.9 - - + +
154C VAL* 2.8 36.6 + - - +
342C LEU* 3.5 8.6 - - - +
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C MET* 3.9 22.1 - - + +
23C SER 3.1 10.0 + - - +
24C VAL* 3.6 23.8 - - + +
25C ILE 3.2 18.0 + - - +
35C LEU* 5.6 3.4 - - + -
39C LEU* 5.1 9.9 - - + -
125C ALA* 1.3 70.4 - - - +
127C VAL* 1.3 60.5 + - - +
128C VAL* 3.4 11.1 + - + -
154C VAL* 3.4 20.9 - - + +
156C VAL* 3.2 32.5 - - + -
334C LEU* 4.4 28.3 - - + +
337C MET* 4.3 2.7 - - + -
338C ILE* 5.3 6.5 - - + -
342C LEU* 5.6 0.7 - - + -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.5 20.6 - - + +
125C ALA* 4.4 3.1 - - + +
126C LEU* 1.3 70.0 - - - +
128C VAL* 1.3 62.7 + - - +
129C VAL* 3.8 14.7 + - + -
135C VAL* 6.5 0.2 - - + -
139C THR* 3.8 25.8 - - + -
143C LEU* 3.8 35.7 - - + -
153C PRO* 3.9 18.6 - - + -
154C VAL 2.8 13.3 + - - +
155C VAL* 3.4 13.1 - - + +
156C VAL* 3.0 25.8 + - - +
185C VAL* 5.7 0.9 - - + -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.2 9.9 - - + -
25C ILE 3.0 6.9 + - - -
26C ALA* 3.5 23.8 - - + +
30C HIS* 3.6 32.8 + - + +
32C LYS* 5.6 1.1 - - - -
35C LEU* 3.6 23.8 - - + -
126C LEU* 3.9 18.6 - - + +
127C VAL* 1.3 77.0 - - - +
129C VAL* 1.3 67.4 + - - +
139C THR* 4.1 16.3 + - - +
156C VAL* 3.5 8.1 - - + +
158C ASN* 3.7 21.5 - - + -
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS* 4.8 2.7 - - - -
127C VAL* 4.2 13.5 - - + -
128C VAL* 1.3 82.1 - - - +
130C ASP* 1.3 58.5 + - - +
134C GLY 3.1 28.7 - - - +
135C VAL* 3.7 20.2 - - + +
139C THR* 5.1 3.1 - - + -
155C VAL* 4.1 11.7 - - + -
156C VAL 2.8 7.9 + - - +
157C ILE* 3.2 13.3 - - + -
158C ASN* 2.6 34.8 + - - +
181C THR* 3.5 22.9 - - + -
185C VAL* 4.1 11.7 - - + -
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS* 3.5 36.8 + - + +
129C VAL* 1.3 80.3 - - - +
131C THR* 1.3 64.7 + - - +
132C ILE* 2.7 17.4 + - - +
133C GLU* 2.6 33.3 + - + +
134C GLY* 2.8 34.8 + - - +
157C ILE* 4.1 4.5 - - - +
158C ASN* 3.8 3.6 - - - -
159C LYS* 3.2 33.8 - - - +
162C ARG* 5.7 0.3 - - - +
181C THR* 4.6 0.2 + - - -
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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