Contacts of the strand formed by residues 38 - 43 (chain M) in PDB entry 3MQT
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 TYR 38 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LYS* 3.6 24.9 - - + -
31M VAL 3.1 12.1 - - - +
32M THR* 3.6 15.9 - - + +
36M GLY 4.0 12.1 - - - -
37M VAL* 1.3 75.5 - - - +
39M GLY* 1.3 58.4 + - - +
40M LEU* 3.9 34.6 - - + +
112M LEU* 4.0 6.1 - - - -
115M LYS* 2.7 54.1 + - - +
373M LEU* 5.4 1.7 - - - +
375M ILE* 4.0 14.7 - - - +
386M PHE* 3.9 21.3 - + - -
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Residues in contact with GLY 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M LYS* 3.5 6.2 - - - +
31M VAL 3.0 31.0 + - - -
38M TYR* 1.3 75.5 - - - +
40M LEU* 1.3 63.9 + - - +
108M ALA* 3.6 22.7 - - - +
111M ASP* 3.3 9.0 - - - -
112M LEU* 3.7 12.5 - - - +
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Residues in contact with LEU 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 4.0 24.0 - - + -
29M VAL 3.5 0.9 - - - -
30M LYS* 4.3 7.6 - - + -
38M TYR* 3.9 28.9 - - + -
39M GLY* 1.3 81.2 - - - +
41M GLY* 1.3 59.7 + - - +
108M ALA* 3.5 11.8 - - - -
111M ASP* 2.9 23.1 + - - +
115M LYS* 5.5 2.0 - - - +
315M ILE* 4.3 7.2 - - + -
369M LEU* 3.8 12.5 - - - +
371M ILE* 3.9 28.4 - - + +
373M LEU* 4.0 31.0 - - + -
386M PHE* 4.2 12.3 - - + -
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Residues in contact with GLY 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ILE* 3.6 6.9 - - - +
29M VAL* 2.7 38.5 + - - +
40M LEU* 1.3 75.8 - - - +
42M GLU* 1.3 58.8 + - - +
104M GLY 3.7 15.0 - - - -
107M MET* 3.9 8.7 - - - -
108M ALA* 3.5 3.9 - - - +
315M ILE* 3.6 11.9 - - - +
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Residues in contact with GLU 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M THR* 2.7 28.0 + - - +
27M VAL 3.1 15.0 - - - +
29M VAL 4.3 0.9 - - - +
41M GLY* 1.3 74.4 - - - +
43M ALA* 1.3 59.7 + - - +
104M GLY* 3.3 14.9 + - - -
107M MET* 3.6 9.9 - - - +
284M ASN* 3.3 21.3 - - - +
312M LYS* 3.2 6.9 - - + +
313M THR* 2.9 43.3 + - - +
315M ILE* 3.7 14.8 - - + +
316M THR* 2.6 39.3 + - - +
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Residues in contact with ALA 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 4.4 11.4 - - + -
26M THR* 4.4 0.7 + - - -
27M VAL* 3.1 33.9 + - + +
29M VAL* 4.1 16.5 - - + +
42M GLU* 1.3 74.6 - - - +
44M ASP* 1.3 69.3 + - - +
50M MET* 4.8 2.7 - - + -
100M PHE 3.3 25.4 - - - +
101M ALA* 4.4 0.7 - - - -
104M GLY* 4.2 2.0 - - - -
284M ASN* 4.1 3.4 - - - -
312M LYS* 4.1 6.9 + - - -
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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