Contacts of the strand formed by residues 141 - 144 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139J TYR 4.0 0.8 + - - -
140J HIS* 1.3 80.6 - - - +
142J LYS* 1.3 66.2 + - - +
154J THR* 3.6 13.7 - - - -
155J ARG* 4.9 1.6 - - - -
156J HIS* 4.2 15.1 - - - +
141K GLY 4.0 0.3 - - - +
142K LYS* 3.5 7.8 - - - +
143K THR* 3.2 36.6 + - - -
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Residues in contact with LYS 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479I GLU* 3.0 40.8 + - + +
480I TYR* 3.3 42.4 - - + +
483I GLN* 5.8 1.6 - - - +
140J HIS 5.1 1.6 - - - +
141J GLY* 1.3 79.8 - - - +
143J THR* 1.3 64.9 + - - +
144J ILE* 4.1 9.5 + - + +
153J TYR* 3.1 5.5 - - - +
154J THR* 2.7 39.3 + - - +
156J HIS* 5.6 1.6 - - + -
140K HIS* 3.7 31.1 + - + +
141K GLY 3.4 9.2 - - - +
142K LYS* 4.3 0.2 - - - +
143K THR* 3.8 1.8 - - - +
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Residues in contact with THR 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142J LYS* 1.3 75.9 - - - +
144J ILE* 1.3 60.1 + - - +
145J PRO* 3.9 2.1 - - - +
151J PHE* 4.3 9.2 - - + -
152J SER 3.5 8.1 - - - -
153J TYR* 4.2 6.1 - - + -
140K HIS* 3.5 10.4 - - - +
141K GLY* 3.1 26.9 + - - -
142K LYS 3.8 15.5 - - - +
143K THR* 4.0 5.8 - - + -
153K TYR* 3.9 21.5 - - + -
154K THR 3.0 27.2 + - - +
155K ARG* 4.6 7.8 - - - +
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Residues in contact with ILE 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462I GLN* 3.3 48.0 - - + +
463I SER* 3.8 6.3 - - - +
464I PRO* 3.3 28.5 - - + -
480I TYR* 5.0 4.7 - - + -
142J LYS* 4.4 15.7 - - + +
143J THR* 1.3 74.8 - - - +
145J PRO* 1.3 66.0 - - + +
146J ILE* 2.9 25.6 + - + +
150J PHE 5.3 1.4 - - - +
151J PHE* 6.0 0.2 - - - -
152J SER* 2.7 31.1 + - - +
154J THR* 4.1 10.5 - - + -
140K HIS* 4.3 9.4 - - + +
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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