Contacts of the strand formed by residues 346 - 350 (chain C) in PDB entry 3FTN
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 LYS 346 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA* 4.1 3.6 - - - -
36C PRO 2.8 28.9 + - - +
37C CYS* 3.7 6.3 - - - +
38C THR 4.9 0.2 - - - +
60C GLU* 2.9 33.1 + - - -
147C MET* 3.5 28.9 - - + -
151C MET* 3.5 35.4 - - + +
177C ALA* 4.2 6.5 - - + -
319C LEU* 3.0 18.2 + - + +
320C VAL* 3.4 5.0 - - - -
321C THR* 2.9 30.9 + - - -
322C HIS 3.4 3.3 + - - -
337C MET* 4.6 6.6 - - + +
344C LEU* 4.1 0.7 - - - -
345C ILE* 1.3 85.5 - - + +
347C PRO* 1.3 69.5 - - + +
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Residues in contact with PRO 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA* 3.3 9.5 - - - +
36C PRO* 3.3 28.1 - - + +
322C HIS* 3.1 13.0 - - + +
324C PHE* 4.8 1.8 - - + -
333C ALA* 4.1 17.5 - - + +
336C LEU* 4.0 22.9 - - + -
337C MET* 3.5 28.3 - - + -
344C LEU* 3.7 15.0 - - + -
346C LYS* 1.3 90.4 - - + +
348C VAL* 1.3 62.3 + - - +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA* 4.4 9.4 - - + -
34C VAL 3.5 8.1 - - - +
35C ALA* 4.4 1.1 - - + -
143C GLU* 4.2 19.7 - - + +
146C VAL* 3.4 32.5 - - + -
147C MET* 3.8 11.2 - - + -
320C VAL* 3.8 26.9 - - + -
322C HIS 2.8 6.8 + - - +
323C VAL* 3.3 6.6 - - + +
324C PHE* 2.9 25.6 + - - +
347C PRO* 1.3 79.9 - - - +
349C VAL* 1.3 76.6 + - - +
350C ILE* 4.4 5.4 - - + -
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA* 3.2 6.6 - - - +
34C VAL* 2.9 44.8 + - + +
35C ALA* 5.9 1.1 - - - -
36C PRO* 5.9 0.2 - - + -
324C PHE* 3.4 14.8 - - + +
326C GLY 3.4 26.2 - - - +
329C ASN* 3.8 11.0 - - + +
330C ILE* 4.1 13.5 - - + +
333C ALA* 3.5 32.5 - - + -
347C PRO 5.6 0.2 - - - -
348C VAL* 1.3 75.6 - - - +
350C ILE* 1.3 65.2 + - - +
351C LEU* 3.5 16.3 + - + +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.9 5.8 - - - +
33C ALA* 4.6 5.6 - - + +
142C LEU* 5.0 11.9 - - + -
143C GLU* 3.2 30.1 - - - +
323C VAL* 3.5 22.9 - - + -
324C PHE 2.7 14.2 + - - +
325C ARG* 3.4 30.3 + - + +
326C GLY 2.9 26.3 + - - -
348C VAL* 4.4 7.2 - - + -
349C VAL* 1.3 75.4 - - - +
351C LEU* 1.3 61.1 + - - +
352C ALA* 3.0 28.0 - - - +
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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