Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 4FDI
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 ASN 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO 3.7 1.4 + - - +
31A PRO* 1.3 75.1 - - - +
33A ILE* 1.3 61.9 + - - +
133A TYR* 4.4 0.2 - - - -
221A ALA* 5.8 1.1 - - - +
224A HIS 4.2 1.7 - - - +
225A PRO* 3.6 9.0 - - - +
226A PHE* 3.2 61.7 + - + +
277A VAL* 3.3 23.2 - - - +
280A ASN* 2.8 19.2 + - - +
281A THR* 2.8 25.7 + - + +
282A PHE* 2.8 26.3 + - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO 3.7 4.9 - - - +
32A ASN* 1.3 79.0 - - - +
34A LEU* 1.3 61.9 + - - +
35A LEU* 4.1 12.3 - - + -
128A LEU* 4.3 9.4 - - + -
133A TYR* 3.9 24.7 - - + +
226A PHE* 2.8 14.1 + - - +
227A PHE* 3.2 25.6 - - + -
228A LEU 2.9 25.3 + - - -
282A PHE* 3.5 10.3 - - + +
349A SER* 3.5 50.3 - - - +
352A LEU* 4.3 18.4 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN 4.2 0.2 - - - -
33A ILE* 1.3 72.9 - - - +
35A LEU* 1.3 67.3 + - - +
36A LEU* 3.4 34.8 + - + +
217A ILE* 4.1 13.0 - - + -
226A PHE* 4.3 9.6 - - + -
228A LEU* 3.5 31.9 - - + +
230A TRP* 4.6 0.9 - - + -
268A ILE* 3.8 17.7 - - + -
272A LEU* 3.8 29.2 - - + -
281A THR* 4.5 2.9 - - + +
282A PHE 2.8 8.9 + - - +
283A VAL* 3.3 17.4 - - + +
284A PHE 2.9 27.2 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.1 11.4 - - + -
34A LEU* 1.3 75.4 - - - +
36A LEU* 1.3 61.5 + - - +
37A LEU* 3.6 2.3 + - + +
86A LEU* 4.0 28.7 - - + -
124A LEU* 4.2 9.4 - - + -
227A PHE* 3.6 28.7 - - + -
228A LEU 2.8 13.3 + - - +
229A TYR* 3.7 11.4 - - + -
230A TRP* 2.8 32.7 + - - +
282A PHE* 5.1 4.5 - - + -
284A PHE* 3.7 26.7 - - + +
345A LEU* 4.4 22.7 - - + -
349A SER* 4.4 8.7 - - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 30.7 - - + +
35A LEU* 1.3 70.3 - - - +
37A LEU* 1.3 60.1 + - - +
38A MET* 4.0 8.5 - - + -
62A MET* 4.5 10.1 - - + -
230A TRP* 3.6 31.2 - - + -
265A ILE* 3.9 33.9 - - + -
268A ILE* 4.6 8.7 - - + -
269A LEU* 5.4 3.8 - - + -
283A VAL* 5.2 5.8 - - + -
284A PHE 2.8 15.1 + - - +
285A PHE* 3.5 24.9 - - + -
286A THR* 3.0 29.2 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.6 2.3 + - + -
36A LEU* 1.3 72.3 - - - +
38A MET* 1.3 69.9 + - - +
83A ARG* 3.8 27.7 + - + +
86A LEU* 3.8 16.6 - - + -
229A TYR* 3.3 38.4 - - + +
230A TRP 3.0 18.6 + - - +
231A ALA* 3.4 13.5 - - - +
232A VAL 3.6 6.1 + - - +
286A THR* 3.8 19.7 - - + -
287A SER 3.7 29.6 - - - -
288A ASP* 3.8 4.0 - - + +
342A ILE* 3.8 12.6 - - + -
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Residues in contact with MET 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.0 17.7 - - + -
37A LEU* 1.3 84.6 - - - +
39A ASP* 1.3 61.7 + - - +
41A MET* 3.6 25.6 - - + +
83A ARG* 3.9 1.4 + - - -
230A TRP* 4.3 6.1 - - + -
232A VAL* 3.8 21.5 - - + -
235A THR* 5.0 0.2 - - - +
261A ILE* 3.5 30.5 - - + -
265A ILE* 4.2 3.6 - - + -
285A PHE* 3.4 37.7 - - + -
286A THR 2.9 17.0 + - - +
287A SER* 3.9 13.0 - - - -
288A ASP* 3.1 27.2 + - - +
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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