Contacts of the helix formed by residues 2529 - 2534 (chain A) in PDB entry 5ZCS
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 ILE2529 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377A PHE* 5.0 3.6 - - - -
2393A ASP* 4.2 11.9 - - - +
2396A TYR* 3.6 25.1 - - + -
2397A ARG* 3.5 32.3 - - + +
2525A VAL* 3.3 24.2 - - + +
2526A GLU* 3.2 23.2 + - - +
2527A LEU 3.3 0.8 + - - -
2528A LEU* 1.3 77.4 - - - +
2530A LYS* 1.3 60.6 + - + +
2531A GLN 3.2 2.1 + - - -
2532A ALA* 3.5 5.1 + - - +
2533A THR* 2.4 39.8 + - + +
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Residues in contact with LYS2530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2513A PHE* 6.1 1.3 - - - -
2526A GLU* 3.3 42.8 + - - +
2527A LEU* 3.4 33.1 - - - +
2529A ILE* 1.3 78.9 - - + +
2531A GLN* 1.3 63.7 + - - +
2532A ALA 3.3 2.0 + - - -
2533A THR* 3.8 11.7 - - - -
2534A SER* 3.9 19.9 + - - +
2536A GLU* 4.9 3.3 - - - +
170C GLU* 6.1 1.3 - - - +
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Residues in contact with GLN2531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2332A TYR* 5.8 1.9 - - - -
2374A LYS 4.1 6.4 - - - +
2375A ILE* 5.4 0.3 - - - +
2376A PRO* 3.5 35.1 - - - +
2377A PHE* 3.5 14.3 - - - -
2513A PHE* 5.0 14.6 - - + -
2527A LEU 3.3 23.3 + - - +
2528A LEU* 3.9 17.1 + - + +
2530A LYS* 1.3 83.2 - - - +
2532A ALA* 1.3 76.7 + - - +
2534A SER 5.0 1.9 - - - +
2536A GLU* 5.1 2.3 - - - +
2537A ASN* 2.6 35.2 + - - +
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Residues in contact with ALA2532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2375A ILE* 4.7 13.9 - - + -
2376A PRO* 5.0 2.0 - - + -
2377A PHE* 4.4 22.9 - - + +
2379A LEU* 3.3 23.2 - - + +
2529A ILE 3.5 2.2 + - - -
2531A GLN* 1.3 98.8 - - - +
2533A THR* 1.3 64.6 + - - +
2534A SER 3.6 2.7 - - - -
2538A LEU* 3.3 22.0 - - - +
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Residues in contact with THR2533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379A LEU* 3.9 22.2 - - + +
2392A LEU* 5.8 8.1 - - + -
2529A ILE* 2.4 34.3 + - + +
2530A LYS* 3.8 10.4 - - - -
2532A ALA* 1.3 76.5 - - - +
2534A SER* 1.3 66.9 + - - +
2535A HIS* 3.6 14.2 + - - -
2538A LEU* 5.0 0.2 - - - +
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Residues in contact with SER2534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2530A LYS* 3.9 12.2 + - - -
2531A GLN 5.0 2.8 - - - +
2532A ALA* 3.8 3.0 - - - +
2533A THR* 1.3 85.9 - - - +
2535A HIS* 1.3 61.6 + - - +
2536A GLU* 2.5 30.5 + - - -
2537A ASN* 4.3 2.3 + - - +
2538A LEU* 3.4 18.4 - - - +
222C TYR* 2.3 30.9 + - - -
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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