Contacts of the strand formed by residues 118 - 123 (chain D) in PDB entry 1ZMC
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 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LYS* 3.6 36.3 - - + +
117D GLY* 1.3 69.4 - - - -
119D GLY* 1.3 67.7 + - - +
120D LYS* 3.7 4.8 + - + +
128D THR 3.3 4.0 - - - +
129D ALA* 4.1 0.7 - - - -
130D THR* 2.9 38.0 + - - +
283D PHE* 3.3 20.4 - + - -
285D LYS* 2.6 32.9 + - - +
286D ASN* 3.7 27.9 + - + -
480D FAD 3.5 19.3 - - - -
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Residues in contact with GLY 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.5 3.1 - - - -
35D ILE* 4.1 14.4 - - - -
117D GLY 3.6 3.2 + - - -
118D TYR* 1.3 78.8 - - - +
120D LYS* 1.3 61.5 + - - +
127D VAL* 4.3 9.0 - - - -
128D THR 3.6 4.7 - - - -
129D ALA* 4.3 1.6 - - - -
286D ASN 4.1 0.5 - - - +
287D LEU* 3.6 10.0 - - - +
480D FAD 2.8 39.3 + - - -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D TYR* 4.7 4.7 - - + +
119D GLY* 1.3 75.7 - - - +
121D ILE* 1.3 71.4 + - - +
122D THR* 3.0 23.7 + - + +
127D VAL* 3.9 5.3 - - - +
128D THR* 2.9 35.5 + - - +
286D ASN* 3.1 30.1 - - + +
287D LEU* 3.5 8.1 - - - +
288D GLY* 4.3 7.8 - - - +
291D GLU* 3.4 24.9 + - - -
2013D SO4 5.4 0.9 - - - -
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.2 15.9 - - + -
120D LYS* 1.3 73.2 + - - +
122D THR* 1.3 59.5 + - - +
123D GLY 3.1 23.3 - - - +
126D GLN 3.7 6.1 - - - +
127D VAL* 4.5 1.6 - - + +
144D ILE* 4.0 31.0 - - + -
146D ILE* 4.1 21.5 - - + -
287D LEU* 2.7 28.4 + - + +
288D GLY* 4.2 11.3 - - - +
289D LEU* 4.7 1.8 - - + -
291D GLU* 5.2 2.3 - - - +
292D LEU* 3.4 39.4 - - + +
315D ILE* 4.3 7.4 - - + -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LYS* 3.0 30.2 + - + +
121D ILE* 1.3 73.4 - - - +
123D GLY* 1.3 56.6 + - - +
126D GLN* 2.6 42.7 + - - +
128D THR* 2.8 32.3 + - + +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 3.1 18.1 + - - +
122D THR* 1.3 77.7 - - - +
124D LYS* 1.3 66.6 + - - -
125D ASN 3.0 3.8 - - - -
126D GLN* 3.1 23.9 + - - +
144D ILE* 4.0 0.3 - - - +
292D LEU* 4.6 5.9 - - - +
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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