Contacts of the strand formed by residues 256 - 264 (chain D) 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 VAL 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235D GLY* 5.3 0.4 - - - -
236D VAL* 3.3 13.7 - - - +
237D ASP 3.4 21.8 - - - +
238D ARG* 4.0 2.9 - - - +
239D VAL* 3.9 17.9 - - + -
252D ALA 3.0 17.4 + - - +
253D VAL* 3.7 15.1 - - + +
254D LYS 3.5 3.0 - - - +
255D MET* 1.3 81.8 - - - +
257D LYS* 1.3 75.5 + - - +
258D PRO* 3.9 2.4 - - - +
260D GLY* 4.1 9.6 - - - -
261D ILE 4.1 6.7 - - - +
262D ILE* 4.2 15.9 - - + -
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Residues in contact with LYS 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.0 26.1 - - - +
304C ARG* 5.0 1.8 - - - +
169D SER* 4.7 1.2 + - - -
234D LYS* 3.3 45.1 - - - +
235D GLY* 3.5 22.0 - - - -
236D VAL 2.8 19.6 + - - +
237D ASP* 2.8 38.6 + - - +
255D MET 3.8 0.2 + - - -
256D VAL* 1.3 81.6 - - - +
258D PRO* 1.3 76.2 - - + +
260D GLY* 2.9 23.7 + - - +
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Residues in contact with PRO 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLU* 6.3 0.7 - - + -
97B ARG* 3.2 29.9 + - - +
99B TYR* 4.9 2.4 - - - +
102B HIS* 3.7 34.8 - - + +
105B GLY* 5.0 0.9 - - - -
106B MET* 3.9 38.1 - - + +
256D VAL 3.9 2.4 - - - +
257D LYS* 1.3 88.2 - - + +
259D GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.6 4.0 + - - -
99B TYR* 3.5 52.2 + - - -
102B HIS* 4.6 5.2 + - - -
238D ARG* 4.3 7.3 + - - -
258D PRO* 1.3 71.6 - - - +
260D GLY* 1.3 64.2 + - - +
261D ILE* 4.6 4.0 - - - +
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Residues in contact with GLY 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.9 1.5 - - - +
237D ASP* 3.4 16.2 - - - -
238D ARG* 3.9 4.0 - - - -
256D VAL* 4.1 6.1 - - - -
257D LYS* 2.9 23.3 + - - -
258D PRO 3.1 0.8 - - - -
259D GLY* 1.3 83.3 + - - +
261D ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TYR* 6.1 0.2 - - - +
161D LEU 3.9 17.0 - - - +
162D ALA* 3.5 19.4 - - - +
163D ASP* 3.7 22.4 - - + +
237D ASP 3.5 6.9 + - - -
238D ARG* 3.5 28.6 - - - +
239D VAL 3.1 23.9 + - - +
256D VAL* 4.1 2.0 - - - +
259D GLY 4.6 3.6 - - - +
260D GLY* 1.3 78.6 - - - +
262D ILE* 1.3 75.7 + - - +
263D SER* 4.6 1.0 - - - +
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Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D VAL* 3.4 9.6 - - + +
241D MET* 3.6 33.2 - - + -
249D LEU* 4.3 8.3 - - + -
252D ALA* 3.9 17.3 - - + +
253D VAL* 3.6 45.3 - - + +
256D VAL* 4.2 13.5 - - + -
261D ILE* 1.3 83.9 - - - +
263D SER* 1.3 63.1 + - - +
264D ASN* 4.0 2.3 + - + +
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Residues in contact with SER 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D GLY* 2.7 35.8 + - - -
161D LEU* 3.4 20.5 - - - +
162D ALA* 3.9 20.2 - - - -
239D VAL 2.7 14.3 + - - -
240D ILE* 3.2 7.4 - - - +
241D MET 2.7 29.7 + - - -
261D ILE* 4.0 0.6 - - - -
262D ILE* 1.3 73.8 - - - +
264D ASN* 1.3 55.7 + - - +
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Residues in contact with ASN 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TRP* 4.6 16.2 - - + -
284B GLY* 3.1 36.3 + - - +
161D LEU* 4.4 10.8 - - - +
241D MET* 3.4 27.0 - - + +
262D ILE* 4.0 3.4 + - + +
263D SER* 1.3 73.1 + - - +
265D ILE* 1.3 66.3 + - - +
266D ASN* 3.1 36.2 + - - +
268D HIS* 2.8 26.9 + - - -
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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