Contacts of the strand formed by residues 141 - 144 (chain I) in PDB entry 1ZUM
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 141 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I TYR 4.0 0.8 + - - -
140I HIS* 1.3 79.3 - - - +
142I LYS* 1.3 64.0 + - - +
154I THR* 3.5 14.1 - - - -
155I ARG* 4.8 1.3 - - - -
156I HIS* 4.0 15.5 + - - +
141L GLY 3.9 0.5 - - - +
142L LYS* 3.4 7.6 - - - +
143L THR* 3.1 36.1 + - - -
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Residues in contact with LYS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I HIS 5.2 2.5 + - - +
141I GLY* 1.3 77.3 - - - +
143I THR* 1.3 62.3 + - - +
144I ILE* 3.9 9.1 - - + +
153I TYR* 3.1 5.4 - - - +
154I THR* 2.7 43.5 + - - +
156I HIS* 5.4 2.1 - - - -
479J GLU* 3.6 38.0 + - + +
480J TYR* 3.3 42.4 - - + +
140L HIS* 3.7 37.4 + - + +
141L GLY 3.4 5.6 - - - +
142L LYS* 4.4 0.2 - - - +
143L THR* 3.9 1.7 - - - +
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Residues in contact with THR 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I LYS* 1.3 76.7 - - - +
144I ILE* 1.3 61.0 + - - +
145I PRO* 3.9 2.1 - - - +
151I PHE* 4.2 9.2 - - + -
152I SER 3.5 7.4 - - - -
153I TYR* 4.1 7.2 - - + -
140L HIS* 3.4 10.6 - - - +
141L GLY* 3.1 27.2 + - - -
142L LYS 3.8 15.9 - - - +
143L THR* 4.0 5.8 - - + -
153L TYR* 3.9 19.7 - - + -
154L THR 3.0 28.2 + - - +
155L ARG* 4.6 7.2 - - - +
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Residues in contact with ILE 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I LYS* 4.3 11.7 - - + +
143I THR* 1.3 76.0 - - - +
145I PRO* 1.3 65.0 - - + +
146I ILE* 2.9 11.3 + - - +
150I PHE 5.3 0.7 - - - +
151I PHE* 5.9 0.2 - - - -
152I SER* 2.7 33.2 + - - +
154I THR* 3.9 16.8 - - + +
490I THR* 5.4 0.2 - - + -
462J GLN* 3.3 44.9 - - + +
463J SER* 4.0 13.0 - - - +
464J PRO* 3.4 35.2 - - + -
480J TYR* 4.9 2.7 - - + -
140L HIS* 4.0 14.8 - - + +
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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