Contacts of the strand formed by residues 22 - 29 (chain B) in PDB entry 2O7M
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 SER 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.8 1.0 - - - +
20B ASP 5.0 0.9 + - - -
21B GLY* 1.3 75.9 + - - -
23B ILE* 1.3 65.1 - - - +
24B ILE* 4.0 24.8 - - - +
42B THR 3.8 0.9 - - - +
43B PHE* 3.4 6.3 - - - -
44B GLN* 2.9 50.3 + - - +
98B LYS* 5.0 1.6 - - - +
136B ASN* 6.0 0.9 - - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.2 17.0 - - + -
22B SER* 1.3 76.5 - - - +
24B ILE* 1.3 61.2 + - - +
42B THR 3.6 6.5 - - - +
43B PHE* 4.1 14.1 - - + -
88B LEU* 4.1 20.9 - - + -
91B LEU* 5.4 0.2 - - + -
95B LEU* 4.1 9.0 - - + -
98B LYS* 4.0 29.2 - - + +
101B GLN* 4.0 18.2 - - + +
102B ALA* 4.1 17.5 - - + +
105B VAL* 3.6 28.0 - - + -
132B ILE* 3.6 7.9 - - - +
136B ASN* 2.9 25.6 + - - +
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Residues in contact with ILE 24 (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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22B SER* 4.0 24.5 - - - +
23B ILE* 1.3 78.7 - - - +
25B ALA* 1.3 64.0 + - - +
26B GLN* 3.8 32.5 - - + +
41B LEU* 3.5 4.5 - - - +
42B THR* 2.9 42.9 + - - +
44B GLN* 4.7 10.8 - - + +
105B VAL* 4.7 4.7 - - - +
132B ILE* 4.4 1.6 - - - -
136B ASN* 3.9 15.5 - - + +
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Residues in contact with ALA 25 (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 ILE* 1.3 74.8 - - - +
26B GLN* 1.3 69.4 + - - +
39B LEU* 4.4 0.2 - - + -
40B SER 3.3 7.2 - - - -
41B LEU* 3.5 23.1 - - + -
108B ILE* 4.2 0.4 - - + -
129B VAL* 3.6 32.1 - - + +
132B ILE* 3.8 29.5 - - + +
133B ALA* 5.9 2.4 + - - +
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Residues in contact with GLN 26 (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 ILE* 3.8 22.1 - - + +
25B ALA* 1.3 79.8 - - - +
27B ILE* 1.3 63.6 + - - +
28B LYS* 4.1 24.7 - - + +
38B GLN 3.6 0.7 - - - +
39B LEU* 3.3 8.5 - - - +
40B SER* 2.8 49.3 + - - +
42B THR* 4.6 8.3 + - - -
129B VAL* 4.1 4.0 - - - -
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Residues in contact with ILE 27 (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 GLN* 1.3 72.9 - - - +
28B LYS* 1.3 65.8 + - - +
29B PRO* 4.7 1.0 - - - +
37B HIS* 3.6 33.0 - - + -
38B GLN 3.5 1.8 - - - +
39B LEU* 3.8 35.9 - - + -
122B PHE* 4.1 17.9 - - + -
125B VAL* 4.6 3.4 - - + -
126B CYS* 4.1 24.2 - - + -
129B VAL* 3.8 25.7 - - + +
142B LYS* 4.6 13.5 + - - -
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Residues in contact with LYS 28 (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 GLN* 4.5 26.2 - - + +
27B ILE* 1.3 80.5 - - - +
29B PRO* 1.4 74.5 - - + +
37B HIS* 3.2 6.3 - - - -
38B GLN* 2.8 55.6 + - + +
40B SER* 4.4 16.6 + - - +
154B SER* 4.7 9.6 - - - +
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Residues in contact with PRO 29 (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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27B ILE 4.7 1.3 - - - +
28B LYS* 1.4 90.8 - - + +
30B ASN* 1.3 62.9 + - - +
31B GLN* 4.6 8.3 - - - +
36B LYS 3.6 8.7 - - - +
37B HIS* 3.7 15.7 - - + +
38B GLN* 5.2 1.4 + - - -
142B LYS* 5.9 1.6 - - - +
147B THR 5.1 0.2 - - - +
150B ALA* 3.7 28.9 - - + +
151B VAL* 3.7 36.3 - - + -
154B SER* 3.5 28.1 + - - +
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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