Contacts of the strand formed by residues 325 - 333 (chain B) in PDB entry 3POS
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 THR 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU 3.4 2.1 - - - +
67B GLN* 3.1 3.3 - - - -
68B THR* 3.0 27.2 + - - -
97B VAL* 3.7 12.1 - - + -
98B LYS 3.3 7.9 - - - +
99B HIS* 2.7 39.0 + - + +
101B GLN* 2.9 10.1 + - - +
320B GLN* 2.9 24.2 + - - -
324B GLY* 1.3 78.3 - - - +
326B ILE* 1.3 63.7 + - - +
327B PHE* 3.7 28.2 - - + -
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Residues in contact with ILE 326 (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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52B SER 3.7 18.8 - - - +
53B SER* 3.7 6.3 - - - +
54B GLY 3.7 27.4 - - - +
63B ASP 4.4 6.5 - - - +
65B GLY* 3.8 21.8 - - - +
66B LEU 3.3 3.1 - - - +
67B GLN* 3.7 24.7 - - + +
96B THR* 3.9 0.7 + - - +
97B VAL* 3.5 4.2 - - - -
98B LYS* 2.9 53.6 + - + +
100B GLU* 3.8 14.8 - - - +
324B GLY 3.8 2.5 - - - +
325B THR* 1.3 77.5 - - - +
327B PHE* 1.3 63.7 - - - +
328B ASP* 5.0 3.5 - - + +
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Residues in contact with PHE 327 (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 PHE* 3.7 3.3 - - - -
49B PHE* 4.0 24.2 - + - -
65B GLY* 3.2 5.0 - - - -
66B LEU* 2.8 44.1 + - + +
68B THR* 4.4 6.3 - - + -
95B PHE* 4.5 7.2 - + - -
96B THR 3.5 3.8 - - - -
97B VAL* 4.1 16.6 - - + -
107B GLY 4.1 2.5 - - - -
108B GLY* 3.7 38.1 - - - -
316B LEU* 3.9 24.0 - - + -
318B LEU* 3.9 15.0 - - + -
325B THR* 3.7 26.9 - - + -
326B ILE* 1.3 72.9 - - - +
328B ASP* 1.3 61.6 + - - +
330B PHE* 3.6 19.1 - + + -
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Residues in contact with ASP 328 (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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2B CA 2.4 30.7 - - - -
26B GLN 3.2 9.2 - - - +
27B PHE* 3.5 10.5 - - - -
62B LYS 3.3 8.1 - - - +
63B ASP* 3.7 12.0 - - - +
64B LYS 3.0 12.8 - - - +
65B GLY* 4.3 2.0 - - - -
95B PHE* 3.7 4.0 - - - +
96B THR* 2.9 38.4 + - - +
326B ILE* 4.3 5.1 - - + -
327B PHE* 1.3 75.8 - - - +
329B ASN* 1.3 95.5 + - - +
330B PHE* 3.3 7.3 + - - -
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Residues in contact with ASN 329 (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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2B CA 4.4 1.6 - - - -
25B GLU 3.2 9.3 + - - -
26B GLN* 3.4 36.7 - - - +
62B LYS 5.2 1.9 + - - +
63B ASP* 5.1 1.9 - - - +
94B GLN* 3.6 4.2 + - - +
95B PHE* 3.4 12.8 + - - -
96B THR* 3.9 16.3 + - + +
169B THR* 6.0 0.2 - - - +
171B LEU* 5.4 0.6 - - + +
328B ASP* 1.3 105.2 + - - +
330B PHE* 1.3 64.8 + - - +
331B LEU* 3.6 1.6 + - - +
342B PHE* 4.1 10.1 - - + -
346B THR* 3.5 37.0 - - + +
350B THR* 5.0 4.5 + - - -
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Residues in contact with PHE 330 (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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23B PHE* 3.7 21.3 - + + -
24B LYS* 3.2 9.1 - - - +
25B GLU* 2.9 43.9 + - + +
27B PHE* 3.8 28.0 - + - -
37B TRP* 4.0 13.7 - + - -
94B GLN 3.4 4.7 - - - +
95B PHE* 3.6 19.5 - + + -
110B VAL* 3.7 24.5 - - + -
314B LEU* 3.9 25.1 - - + -
316B LEU* 4.1 10.8 - - + -
327B PHE* 3.6 28.3 - - + -
328B ASP 4.1 7.0 - - - -
329B ASN* 1.3 74.6 - - - +
331B LEU* 1.3 59.8 + - - +
342B PHE* 4.3 0.7 - - - -
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Residues in contact with LEU 331 (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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21B VAL* 3.9 9.2 - - + -
23B PHE 3.4 15.0 - - - +
24B LYS* 3.8 28.5 - - + -
92B VAL* 3.8 0.7 - - + +
93B VAL* 3.5 2.8 - - - +
94B GLN* 2.8 49.2 + - + +
314B LEU* 6.1 0.2 - - - +
329B ASN 4.5 0.7 - - - +
330B PHE* 1.3 76.5 - - - +
332B ILE* 1.3 67.3 + - - +
333B THR* 3.8 17.3 - - + -
338B TYR* 3.9 13.9 - - + -
339B ALA* 3.7 31.0 - - + -
342B PHE* 3.7 31.2 - - + -
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Residues in contact with ILE 332 (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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21B VAL* 3.7 1.6 - - - +
22B TYR* 2.9 26.9 + - + -
23B PHE* 2.9 30.2 + - + +
81B PHE* 3.6 34.1 - - + -
84B PHE* 3.8 18.8 - - + -
91B LEU* 3.8 21.8 - - + -
92B VAL 3.3 9.9 - - - +
93B VAL* 4.4 13.7 - - + -
112B LEU* 3.6 23.8 - - + -
314B LEU* 4.0 10.8 - - + -
331B LEU* 1.3 77.7 - - - +
333B THR* 1.3 62.4 + - - +
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Residues in contact with THR 333 (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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19B PRO* 4.5 0.2 - - - +
20B ALA 2.6 25.0 + - - -
21B VAL* 4.6 2.0 - - - -
22B TYR* 3.9 8.3 - - - -
91B LEU* 3.6 4.9 - - - +
92B VAL* 2.8 47.9 + - + +
331B LEU* 3.8 28.0 - - + -
332B ILE* 1.3 75.1 - - - +
334B ASN* 1.3 59.0 + - - +
335B ASP* 3.3 33.4 + - - +
338B TYR* 4.1 11.1 - - + -
339B ALA* 4.0 3.1 - - + +
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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