Contacts of the strand formed by residues 121 - 125 (chain D) in PDB entry 1ZQ1
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 121 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.4 13.2 - - + +
31D PHE* 3.2 35.7 - + - -
96D PRO* 3.2 30.5 - - + +
119D VAL* 3.9 12.3 + - + -
120D TYR* 1.3 75.0 - - - +
122D MET* 1.3 67.7 + - - +
137D ARG* 3.7 11.7 - - + -
138D THR 2.8 30.7 - - - -
139D ALA* 3.3 15.0 - - + -
141D ILE* 6.0 0.7 - - + -
161D LEU* 2.5 33.9 + - + +
434D PRO* 4.0 1.0 - - - +
435D GLU* 3.0 38.1 + - + +
438D ILE* 4.7 16.9 + - + +
440D PRO* 6.1 0.2 - - - +
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Residues in contact with MET 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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50B LYS* 4.3 7.4 - - - +
54B GLY 3.0 27.4 - - - +
55B TYR* 4.1 19.3 - - + -
56B ASN* 3.5 47.6 - - - +
120D TYR 4.3 4.0 - - - +
121D TYR* 1.3 86.2 - - - +
123D ARG* 1.3 66.3 + - - +
124D LYS 4.1 0.2 - - - -
137D ARG* 3.3 7.8 - - - +
138D THR* 2.8 33.5 + - - +
432D MET* 4.1 24.5 - - + -
433D TYR* 4.0 7.9 - - - -
434D PRO* 4.3 17.3 - - + -
435D GLU* 3.9 3.5 - - - +
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Residues in contact with ARG 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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209B ASP* 4.1 3.6 + - - -
210B ARG* 2.6 37.7 - - - +
122D MET* 1.3 78.3 - - - +
124D LYS* 1.3 62.6 + - - +
125D ILE 3.7 0.3 + - - -
135D PHE* 3.4 38.4 - - + -
136D GLN 3.5 4.5 - - - -
137D ARG* 4.9 0.4 - - + -
431D ARG 3.6 1.0 - - - +
432D MET* 2.8 27.5 - - - -
433D TYR* 2.7 66.6 + - + +
434D PRO 3.9 8.5 - - - -
435D GLU* 2.9 45.4 + - - +
436D THR* 3.7 15.3 - - - +
437D ASP* 3.5 4.9 + - - +
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Residues in contact with LYS 124 (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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55B TYR* 3.6 20.9 + - - -
122D MET 4.1 0.6 - - - -
123D ARG* 1.3 72.3 - - - +
125D ILE* 1.3 69.9 + - - +
126D VAL* 3.6 4.5 - - + +
135D PHE* 3.1 1.9 - - - +
136D GLN* 2.9 61.5 + - + +
138D THR* 3.8 6.0 + - - +
162D GLU* 3.4 17.0 + - - -
189D GLU* 4.4 7.1 + - - -
430D ALA* 3.6 30.7 - - + -
432D MET* 3.7 19.9 - - + +
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Residues in contact with ILE 125 (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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109B TYR* 4.0 22.9 - - + +
211B PRO* 4.2 25.4 - - + -
53D THR* 5.5 0.9 - - - +
123D ARG 4.6 0.9 - - - +
124D LYS* 1.3 79.2 - - - +
126D VAL* 1.3 70.7 + - - +
127D ILE* 4.2 4.9 + - + +
134D GLY 3.6 8.7 - - - +
135D PHE* 4.3 8.7 - - + -
430D ALA* 5.6 1.7 - - - +
431D ARG* 3.0 26.8 + - + +
433D TYR* 3.8 30.3 - - + -
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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