Contacts of the strand formed by residues 388 - 392 (chain D) in PDB entry 1MPX
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 VAL 388 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D TYR* 3.6 20.9 - - - +
333D LEU* 3.4 19.5 - - + +
386D PRO* 3.7 5.1 - - - +
387D PRO* 1.3 83.2 - - + +
389D PHE* 1.3 62.1 + - - +
390D ILE* 3.8 27.1 - - + -
399D ASP 3.4 3.6 - - - +
400D ARG* 3.6 3.3 - - - -
401D LEU* 3.0 41.8 + - + +
402D LYS 4.4 0.4 - - - -
403D ALA* 3.7 25.4 - - - +
404D TRP* 3.9 18.4 - - + -
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Residues in contact with PHE 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D LEU 2.9 12.5 + - - +
334D VAL* 3.2 13.0 - - + -
335D MSE 3.0 22.3 + - - -
362D GLN* 5.4 2.5 - - + -
363D PHE* 4.2 23.3 - + - -
366D ASP* 5.8 1.3 - - + -
367D VAL* 3.8 27.1 - - + -
386D PRO* 3.9 22.9 + - + +
388D VAL* 1.3 72.5 - - - +
390D ILE* 1.3 60.6 + - - +
398D TRP* 3.2 76.0 - + + -
399D ASP 3.5 7.6 - - - -
400D ARG* 3.9 29.8 - - + -
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Residues in contact with ILE 390 (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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305D LEU* 4.5 6.7 - - + -
333D LEU* 5.4 0.2 - - + -
335D MSE 3.4 35.2 - - + +
388D VAL* 3.8 20.4 - - + -
389D PHE* 1.3 75.3 - - - +
391D TYR* 1.3 64.9 + - - +
398D TRP* 3.6 4.4 - - - -
399D ASP* 2.8 44.4 + - + +
401D LEU* 4.0 12.1 - - + -
404D TRP* 3.5 40.6 - - + -
575D ASN* 3.6 24.9 + - + +
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Residues in contact with TYR 391 (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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305D LEU* 3.5 11.5 - - + +
335D MSE 3.1 10.0 + - - +
336D GLY 4.3 0.7 - - - -
337D PRO* 3.5 45.3 - - + -
355D PHE* 3.6 9.1 - + + +
356D GLU* 3.2 22.1 + - + +
359D THR* 3.7 15.7 - - + -
390D ILE* 1.3 72.1 - - - +
392D ASN* 1.3 88.0 + - - +
393D THR* 3.9 5.2 - - + -
396D ASN* 2.8 34.9 + - - -
397D HIS* 3.5 27.4 - - - -
398D TRP* 3.5 28.7 - + + -
575D ASN* 3.1 19.7 + - - +
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Residues in contact with ASN 392 (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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390D ILE 3.8 0.4 + - - -
391D TYR* 1.3 73.8 - - - +
393D THR* 1.3 57.3 + - - +
394D GLY 3.0 15.2 + - - -
395D GLU* 3.1 23.7 + - + +
396D ASN* 2.9 32.1 + - - -
397D HIS* 2.9 25.7 + - + +
399D ASP* 4.0 9.7 + - - +
495D GLN* 3.7 18.8 - - - +
575D ASN* 3.1 21.3 + - - +
577D THR* 3.2 30.8 + - - +
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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