Contacts of the strand formed by residues 42 - 49 (chain B) in PDB entry 1X1O
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ASP 3.3 6.1 + - - +
41B LEU* 1.3 91.1 - - - +
43B GLY* 1.3 65.8 + - - +
94B ARG* 3.7 26.5 - - - +
95B GLY* 3.6 25.7 - - - +
96B PRO* 4.4 1.8 - - + -
97B LEU* 4.6 0.4 - - - +
286B PRO* 5.8 2.4 - - - +
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Residues in contact with GLY 43 (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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41B LEU 4.0 0.4 + - - -
42B GLU* 1.3 81.5 - - - +
44B GLU* 1.3 62.0 + - - +
94B ARG* 3.4 6.8 - - - +
95B GLY 2.9 33.9 + - - +
97B LEU* 3.9 18.7 - - - +
100B ILE* 3.9 5.3 - - - +
283B VAL* 6.0 0.2 - - - -
284B VAL 5.7 2.0 - - - -
286B PRO* 6.2 2.7 - - - -
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Residues in contact with GLU 44 (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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43B GLY* 1.3 74.6 - - - +
45B ALA* 1.3 62.7 + - - +
92B ARG* 2.9 45.9 + - + +
93B VAL 3.2 15.0 - - - +
94B ARG* 4.3 18.2 + - + -
97B LEU* 5.1 2.4 - - - +
100B ILE* 4.5 2.4 - - - +
283B VAL* 3.5 4.5 - - - +
284B VAL* 2.6 53.2 + - + +
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Residues in contact with ALA 45 (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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44B GLU* 1.3 75.4 - - - +
46B VAL* 1.3 64.3 - - - +
47B ILE 4.3 0.2 + - - -
92B ARG* 3.3 6.8 - - - +
93B VAL* 2.9 47.2 + - + +
100B ILE* 4.0 8.3 - - + -
281B LEU* 3.4 31.4 - - + -
282B LEU 3.2 11.0 - - - +
283B VAL* 4.0 4.9 - - + -
284B VAL 4.2 0.7 - - - +
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Residues in contact with VAL 46 (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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45B ALA* 1.3 80.1 - - - +
47B ILE* 1.3 70.4 + - - +
48B LEU* 3.7 15.5 + - + +
89B GLU* 3.5 34.8 - - + +
91B ALA 3.5 9.6 - - - +
92B ARG* 3.6 35.0 - - + +
280B SER 3.6 0.7 - - - +
281B LEU* 3.3 2.1 - - - -
282B LEU* 2.8 38.5 + - + +
284B VAL* 4.1 12.1 - - + -
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Residues in contact with ILE 47 (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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45B ALA 5.7 1.1 - - - +
46B VAL* 1.3 77.1 - - - +
48B LEU* 1.3 65.2 + - - +
65B PHE* 4.4 12.3 - - + -
74B PHE* 3.8 31.2 - - + -
90B VAL* 2.8 45.5 + - + -
91B ALA* 2.9 20.6 + - + +
93B VAL* 5.7 3.4 - - + -
107B ALA* 6.0 0.7 - - + -
108B LEU* 4.4 15.3 - - + -
111B LEU* 3.9 22.4 - - + -
279B LEU* 4.6 7.0 - - + -
280B SER 3.1 10.5 - - - +
281B LEU* 4.2 19.1 - - + -
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Residues in contact with LEU 48 (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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46B VAL* 3.9 10.5 - - + +
47B ILE* 1.3 76.3 - - - +
49B ALA* 1.3 63.4 + - - +
50B LYS* 3.6 16.4 + - + +
87B GLY* 4.1 12.8 - - - +
88B THR 3.5 7.2 - - - +
89B GLU* 3.7 31.2 - - + +
90B VAL* 4.4 0.7 - - - -
279B LEU* 3.3 9.8 - - - +
280B SER* 2.8 45.0 + - - +
282B LEU* 4.5 28.9 - - + -
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Residues in contact with ALA 49 (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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48B LEU* 1.3 74.4 - - - +
50B LYS* 1.3 61.1 + - - +
51B GLU 3.3 17.9 - - - +
84B VAL* 3.7 25.1 - - + -
85B ALA 3.9 7.2 - - - +
87B GLY* 2.8 27.7 + - - -
88B THR 3.0 16.2 + - - +
90B VAL* 4.0 4.9 - - + +
277B LEU* 5.5 0.4 - - + -
279B LEU* 3.5 18.2 - - + -
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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