Contacts of the strand formed by residues 34 - 41 (chain B) in PDB entry 2XMR
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 GLY 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 4.7 0.7 - - - -
31B THR* 2.6 46.5 + - - +
32B PRO 3.6 0.6 - - - -
33B TYR* 1.3 78.7 - - - +
35B SER* 1.3 62.6 + - - -
89B PRO* 6.4 0.4 - - - -
102B TYR* 4.6 9.6 - - - -
113B MET* 3.4 2.5 - - - +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER* 3.3 21.1 + - - -
29B VAL 3.4 12.5 + - - -
30B GLU* 4.3 7.9 + - - +
34B GLY* 1.3 74.8 - - - -
36B VAL* 1.3 59.6 + - - +
37B THR* 5.9 1.1 - - - -
89B PRO* 3.8 21.8 - - - +
102B TYR* 5.6 0.2 + - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.2 4.1 - - - -
29B VAL* 2.9 53.7 + - + +
31B THR* 4.0 10.8 - - + -
35B SER* 1.3 75.4 - - - +
37B THR* 1.3 66.6 + - - +
38B PHE* 4.0 2.7 - - + -
54B TYR* 5.2 2.2 - - + +
86B VAL* 4.0 18.8 - - + -
87B ASP 3.5 17.5 - - - +
89B PRO* 4.3 15.0 - - + -
113B MET* 4.2 20.2 - - + -
117B VAL* 3.8 18.4 - - + -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 4.0 19.3 - - + -
27B HIS 3.3 12.1 + - - +
28B SER* 4.1 9.9 - - - -
35B SER* 5.9 1.0 - - - -
36B VAL* 1.3 76.5 - - - +
38B PHE* 1.3 67.4 + - - +
39B THR* 5.5 0.2 - - - +
86B VAL* 3.9 2.9 - - - +
87B ASP* 3.0 36.5 + - - +
89B PRO* 5.9 0.4 - - - +
92B GLU* 3.8 46.7 + - + +
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 3.4 2.4 - - - +
27B HIS* 2.8 54.5 + + + +
29B VAL* 3.6 35.7 - - + -
36B VAL* 4.0 12.3 - - + -
37B THR* 1.3 80.1 - - - +
39B THR* 1.3 63.8 + - - +
40B VAL* 4.1 7.0 - - + -
84B VAL* 3.9 20.4 - - + -
85B HIS 3.3 15.5 - - - +
86B VAL* 4.0 11.2 - - + -
87B ASP* 4.5 1.8 - - - +
117B VAL* 3.8 31.4 - - + -
120B TYR* 3.8 7.4 - + - -
121B LEU* 3.9 26.2 - - + -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 4.6 2.0 - - - -
25B LYS 3.3 29.2 - - - +
26B THR* 3.6 16.0 + - - +
37B THR* 5.5 0.2 - - - +
38B PHE* 1.3 76.5 + - - +
40B VAL* 1.3 62.5 + - - +
41B TYR* 3.8 32.4 + - + +
61B TYR* 5.7 5.0 - - - -
83B ARG 3.6 1.2 - - - +
84B VAL* 3.4 2.0 - - - -
85B HIS* 2.7 44.7 + - - +
87B ASP* 4.8 6.6 + - - -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.1 22.0 + - - -
25B LYS* 3.0 27.9 + - - +
27B HIS* 3.9 20.0 - - + +
38B PHE* 4.1 10.8 - - + -
39B THR* 1.3 76.9 - - - +
41B TYR* 1.3 64.0 + - - +
42B GLY 5.4 1.6 - - - +
82B VAL* 3.5 26.7 - - + -
83B ARG 3.2 3.8 - - - +
84B VAL* 4.5 5.8 - - + -
121B LEU* 3.9 29.8 - - + -
123B PHE* 4.9 6.3 - - + -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 4.3 25.8 - - + +
25B LYS* 5.3 0.7 - - - +
39B THR* 3.8 28.4 - - + +
40B VAL* 1.3 75.7 - - - +
42B GLY* 1.3 61.7 + - - +
61B TYR* 4.3 17.4 + + - -
66B GLN* 4.7 7.3 + - - -
70B GLN* 5.9 0.3 + - - -
82B VAL* 3.5 6.6 - - - +
83B ARG* 2.9 36.9 + - - +
85B HIS* 3.5 31.4 - + - -
1305B ACT 3.6 39.0 - - + +
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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