Contacts of the helix formed by residues 433 - 440 (chain A) in PDB entry 1NTZ
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 ASP 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A GLN* 5.1 1.8 - - - +
431A LEU 3.6 1.8 + - - -
432A PRO* 1.3 76.2 - - - +
434A TYR* 1.3 68.2 + - - +
435A ASN* 2.8 28.8 + - - +
436A ARG* 3.0 18.5 + - + +
437A ILE* 3.0 10.2 + - - +
218C ILE* 5.2 2.1 - - - +
219C PRO* 3.8 27.5 - - + +
222C PRO* 4.4 1.0 - - - +
223C TYR* 2.7 43.1 + - - -
229D VAL* 4.6 2.8 - - - +
230D LEU* 4.4 8.1 - - - +
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Residues in contact with TYR 434 (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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238A GLY 4.0 0.5 - - - -
239A SER* 3.4 14.4 - - - -
240A GLN* 3.2 42.8 + - + +
419A CYS* 3.5 12.5 - - - +
420A PRO* 2.8 48.4 + - + +
422A VAL* 4.1 10.5 - - + -
432A PRO 3.8 0.8 + - - -
433A ASP* 1.3 76.3 + - - +
435A ASN* 1.3 58.4 + - - +
437A ILE* 3.1 6.4 + - + +
438A ARG* 2.8 39.0 + - + -
229D VAL* 4.1 19.2 - - + +
17G SER* 5.2 2.0 - - - -
18G LEU 5.4 0.9 - - - -
19G SER* 3.6 30.1 - - - -
20G PRO* 4.1 15.0 - - + -
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Residues in contact with ASN 435 (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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433A ASP* 2.8 13.3 + - - +
434A TYR* 1.3 74.2 - - - +
436A ARG* 1.3 58.4 + - - +
438A ARG* 3.2 8.7 + - - +
439A SER* 2.8 29.6 + - - -
222C PRO* 4.0 15.7 - - + -
223C TYR* 2.9 25.7 + - - -
226D LYS* 2.8 53.2 + - + +
229D VAL* 3.5 9.0 - - - +
20G PRO* 3.5 26.5 - - - +
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Residues in contact with ARG 436 (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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332A ASP* 5.7 2.6 + - - -
339A GLN* 4.6 1.7 - - - +
432A PRO* 4.9 7.4 - - + -
433A ASP* 3.0 15.5 + - + +
435A ASN* 1.3 75.9 - - - +
437A ILE* 1.3 64.8 + - - +
439A SER* 3.2 9.2 + - - +
440A GLY* 3.0 20.1 + - - -
5C ARG* 3.6 21.8 - - - +
19C ILE* 3.0 33.5 + - - +
20C ASP* 2.9 29.8 + - - -
219C PRO* 3.9 14.7 - - - +
221C HIS* 3.9 19.4 - - + +
222C PRO* 3.8 28.9 - - + -
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Residues in contact with ILE 437 (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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240A GLN* 3.9 17.9 - - - +
255A ILE* 3.5 28.7 - - + -
335A MET* 4.5 15.0 - - + -
339A GLN* 2.8 36.5 + - - +
420A PRO* 4.2 6.3 - - + -
422A VAL* 3.9 23.3 - - + -
431A LEU* 4.7 3.4 - - + -
432A PRO* 3.4 37.7 - - + +
433A ASP 3.0 9.0 + - - +
434A TYR* 3.6 7.4 - - + +
436A ARG* 1.3 75.8 - - - +
438A ARG* 1.3 62.8 + - - +
440A GLY 3.2 4.0 + - - -
441A MET* 3.5 5.2 - - - +
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Residues in contact with ARG 438 (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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417A ASP* 2.7 48.0 + - - -
418A GLN 3.4 20.5 + - - +
419A CYS* 2.9 34.9 - - - +
420A PRO* 4.1 4.5 - - - -
434A TYR* 2.8 30.8 + - + +
435A ASN* 3.2 9.2 + - - +
437A ILE* 1.3 79.1 - - - +
439A SER* 1.3 56.5 + - - +
441A MET* 3.1 24.1 + - - +
442A PHE* 4.0 7.2 - - + -
33E LYS* 3.0 17.3 - - - +
37E TYR* 3.7 4.5 + - - -
20G PRO* 5.2 3.8 - - + -
21G PHE* 3.0 39.1 - - + -
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Residues in contact with SER 439 (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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435A ASN 2.8 16.2 + - - -
436A ARG* 3.2 11.6 + - - -
438A ARG* 1.3 76.3 - - - +
440A GLY* 1.3 56.1 + - - +
441A MET 3.2 1.1 - - - -
442A PHE* 3.2 51.0 - - - +
226D LYS* 4.9 10.0 + - - -
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Residues in contact with GLY 440 (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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339A GLN* 3.6 37.0 - - - +
343A MET* 3.8 14.0 - - - +
436A ARG 3.0 12.0 + - - -
437A ILE 3.2 5.2 + - - -
439A SER* 1.3 75.1 - - - +
441A MET* 1.3 58.3 + - - +
442A PHE 3.3 7.8 + - - +
443A TRP* 5.5 1.6 - - - -
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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