Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 1F5J
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 PHE 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 3.7 22.0 - - + -
27B THR 3.2 15.5 - - - +
28B VAL* 4.1 3.8 - - - -
29B TYR* 3.8 4.9 - - - -
32B GLY 3.7 3.1 - - - -
33B ARG* 1.3 75.4 - - - +
35B SER* 1.3 68.6 + - - +
36B CYS* 4.0 9.0 - - - -
46B PHE* 3.7 36.8 - - + -
48B THR* 3.4 36.1 - - + -
177B LEU* 3.7 15.9 - - + -
179B VAL* 4.2 5.2 - - + -
189B ASN* 3.6 3.8 - - - +
190B ILE* 2.7 75.6 + - + +
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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
----------------------------------------------------------
26B MET* 3.3 5.2 - - - +
27B THR* 3.0 37.0 + - - -
29B TYR* 3.6 20.0 + - - -
34B PHE* 1.3 75.0 - - - +
36B CYS* 1.3 64.2 + - - +
37B GLN* 5.6 4.7 + - - -
188B ALA 3.3 9.9 - - - -
189B ASN* 3.3 21.3 - - - -
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Residues in contact with CYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.2 12.1 - - - +
26B MET* 4.4 0.7 - - + -
34B PHE* 4.0 9.2 - - + -
35B SER* 1.3 77.5 - - - +
37B GLN* 1.3 71.3 + - - +
38B TRP* 4.2 2.0 - - - -
46B PHE* 3.4 50.0 - - + -
179B VAL* 3.9 21.8 - - - -
187B SER* 3.2 0.5 - - - -
188B ALA* 2.9 42.1 + - - +
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Residues in contact with GLN 37 (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 THR* 3.7 0.3 - - - -
25B THR* 3.1 52.6 + - + +
35B SER* 5.6 4.2 + - - -
36B CYS* 1.3 82.1 - - - +
38B TRP* 1.3 66.8 + - - +
46B PHE* 3.6 2.6 - - - -
186B GLY 3.2 8.7 - - - +
187B SER* 3.5 19.7 - - - -
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Residues in contact with TRP 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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23B ASN 3.3 10.5 - - - +
24B THR* 4.3 0.9 - - + -
36B CYS* 4.2 3.1 - - - -
37B GLN* 1.3 80.2 - - - +
39B SER* 1.3 64.4 + - - +
41B ILE* 3.4 26.5 - - + -
44B ALA* 4.8 0.2 - - + -
46B PHE* 3.7 28.9 - + + -
70B TYR* 4.7 1.8 - + - -
72B PRO* 4.2 9.4 - - + -
76B SER* 3.6 26.5 - - - -
179B VAL* 3.6 31.2 - - + -
181B GLY* 3.8 11.4 - - - -
184B SER* 3.3 39.9 + - - -
185B SER* 3.0 10.0 - - - -
186B GLY* 2.9 61.7 + - - +
187B SER* 3.7 16.2 - - - -
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Residues in contact with SER 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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23B ASN* 2.9 40.4 + - - +
38B TRP* 1.3 78.5 - - - +
40B ASN* 1.3 83.0 + - - +
41B ILE* 3.1 4.0 + - - +
184B SER 3.8 7.9 - - - -
185B SER* 3.8 11.4 - - - -
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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
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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