Contacts of the strand formed by residues 41 - 44 (chain B) in PDB entry 1XPM
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 GLU 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.3 44.7 + - + -
17B VAL 3.6 5.2 - - - +
18B ASP* 5.0 6.9 - - - +
19B MET* 4.0 3.8 - - - -
39B GLN* 4.8 2.7 + - - +
40B THR* 1.3 92.9 - - + +
42B MET* 1.3 60.1 + - - +
271B ARG 3.1 5.5 + - - +
272B TYR* 3.0 50.7 - - + +
273B VAL 3.3 5.4 + - - -
274B GLY* 4.2 0.7 + - - -
335B LEU 5.3 0.5 - - - +
338B ARG* 3.1 21.3 + - - -
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Residues in contact with MET 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.0 5.6 - - - -
17B VAL* 2.9 55.7 + - + -
19B MET* 3.8 9.6 - - - +
22B LEU* 3.7 21.1 - - + -
41B GLU* 1.3 71.9 - - - +
43B ALA* 1.3 74.8 + - - +
44B VAL* 3.4 0.9 + - - +
150B GLU 2.9 28.3 - - - +
151B PRO 3.6 17.5 - - - +
153B GLN* 3.4 37.7 - - + +
273B VAL 3.8 3.4 - - - -
274B GLY* 5.4 0.4 - - - -
346B TYR* 4.3 15.0 - - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 5.0 0.9 - - + -
13B PRO* 4.0 12.8 - - + -
15B TYR 3.7 6.7 - - - +
16B TYR* 4.4 2.9 - - - +
41B GLU 4.1 0.2 + - - -
42B MET* 1.3 84.3 - - - +
44B VAL* 1.3 61.2 + - - +
45B SER 4.3 0.5 + - - -
153B GLN* 5.6 0.3 - - - +
154B GLY* 4.2 8.7 + - - -
155B ALA* 3.8 31.0 - - - +
273B VAL* 3.0 29.6 + - + +
338B ARG* 4.5 7.6 - - - +
346B TYR* 5.9 0.5 - - - -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.4 18.3 - - - +
15B TYR* 3.0 28.1 + - + +
16B TYR 3.9 2.9 - - - -
17B VAL* 3.7 27.4 - - + +
42B MET* 3.6 14.4 - - + +
43B ALA* 1.3 74.6 - - - +
45B SER* 1.3 63.6 + - - +
46B PRO* 3.5 5.2 - - - +
341B VAL* 4.2 5.4 - - + -
346B TYR* 4.0 25.4 - - + +
349B PHE* 3.9 36.8 - - + -
350B PHE* 6.3 0.4 - - - -
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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
------------------------------------------------------------
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