Contacts of the strand formed by residues 331 - 336 (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 ASN 331 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 4.1 6.4 - - + +
299D THR* 3.5 2.7 - - - +
301D TRP* 3.1 24.8 + - - -
318D TYR* 3.0 39.6 + - - -
321D MSE 3.6 18.5 - - - +
322D GLU* 2.9 29.5 + - - +
325D ASP* 3.1 15.0 + - + +
329D THR 3.8 0.6 - - - -
330D LEU* 1.3 80.8 - - - +
332D TYR* 1.3 65.1 + - - +
387D PRO 4.3 0.2 - - - +
638D CA 2.2 31.9 - - - -
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Residues in contact with TYR 332 (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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298D PRO* 5.3 0.2 - - + -
299D THR 2.8 19.4 + - - +
300D MSE 4.0 21.5 - - + -
301D TRP* 2.9 24.5 + - - -
318D TYR* 3.4 12.3 - - - -
328D ASN 3.9 6.4 + - - -
329D THR* 3.4 48.7 + - - +
330D LEU 4.0 1.6 - - - -
331D ASN* 1.3 79.3 - - - +
333D LEU* 1.3 62.9 + - - +
334D VAL* 5.5 0.2 - - + -
371D PHE* 3.7 24.4 - + - -
375D TYR* 5.0 2.3 + - - -
385D THR* 3.5 40.4 + - + -
386D PRO 3.3 19.5 - - - +
387D PRO* 3.5 15.9 - - + -
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Residues in contact with LEU 333 (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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301D TRP 3.4 9.0 - - - +
314D ALA* 4.6 3.4 - - + +
315D ILE* 3.9 23.3 - - + +
318D TYR* 3.6 37.9 - - + -
332D TYR* 1.3 76.6 - - - +
334D VAL* 1.3 73.7 + - - +
335D MSE 3.9 24.7 - - + +
386D PRO 5.0 0.5 - - - +
387D PRO 3.2 6.0 + - - +
388D VAL* 3.4 14.3 - - + -
389D PHE* 2.9 24.9 + - - +
390D ILE* 5.4 0.4 - - + -
404D TRP* 3.8 41.5 - - + -
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Residues in contact with VAL 334 (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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300D MSE 3.7 30.5 - - + -
301D TRP 2.9 7.8 + - - +
302D LEU* 3.2 28.9 - - + -
303D GLN 3.1 24.5 + - - +
332D TYR* 5.5 0.2 - - + -
333D LEU* 1.3 81.7 - - - +
335D MSE 1.3 67.3 + - - +
338D TRP* 4.2 13.5 - - + -
363D PHE* 3.8 25.8 - - + -
367D VAL* 5.0 0.7 - - + -
386D PRO 6.1 0.4 - - - +
389D PHE* 3.2 25.8 - - + +
398D TRP* 4.6 1.1 - - + -
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Residues in contact with MSE 335 (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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303D GLN* 3.2 46.9 - - + +
304D GLY 4.6 1.6 - - - +
305D LEU* 4.1 18.0 - - + +
311D MSE 5.9 1.1 - - - -
315D ILE* 3.9 28.9 - - + -
333D LEU* 3.9 18.6 - - + -
334D VAL* 1.3 79.2 - - - +
336D GLY* 1.3 60.9 + - - +
389D PHE 3.0 8.4 + - - -
390D ILE* 3.4 24.2 - - + +
391D TYR* 3.1 24.6 + - - +
398D TRP* 3.8 1.7 - - - -
573D THR* 3.9 36.8 - - - +
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Residues in contact with GLY 336 (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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303D GLN 3.3 8.1 + - - -
304D GLY* 3.6 0.5 - - - -
305D LEU* 2.9 32.5 + - - +
335D MSE 1.3 74.1 - - - +
337D PRO* 1.3 70.0 - - - +
338D TRP* 2.9 26.3 + - - -
391D TYR* 4.2 0.2 - - - -
398D TRP* 3.7 11.9 - - - -
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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