Contacts of the strand formed by residues 205 - 210 (chain H) in PDB entry 1FSK
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 ILE 205 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H ALA* 4.8 10.3 - - + -
113H PRO* 4.4 27.4 - - + +
115H VAL* 3.6 30.6 - - + +
194H CYS 3.8 0.9 - - - +
196H ALA* 2.9 43.9 + - + +
198H HIS* 5.0 7.0 - - + +
200H THR* 5.4 0.4 - - - +
201H SER* 3.9 19.5 - - - +
203H SER 4.4 0.9 - - - +
204H PRO* 1.3 73.2 - - + +
206H VAL* 1.3 67.0 + - - +
207H LYS* 5.1 7.2 - - + -
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Residues in contact with VAL 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H VAL* 5.5 0.4 - - - -
149H LYS* 6.3 0.2 - - - -
193H THR* 3.4 23.8 - - - +
194H CYS 3.4 7.6 - - - +
195H GLU* 2.8 31.9 - - - +
204H PRO* 3.6 12.7 + - + +
205H ILE* 1.3 77.5 - - - +
207H LYS* 1.3 87.5 + - - +
208H SER* 5.2 2.2 - - - +
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Residues in contact with LYS 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H VAL* 3.7 49.4 + - + +
116H SER* 4.5 1.5 - - - +
117H ILE* 3.9 17.6 - - + +
194H CYS* 2.6 41.5 + - + +
205H ILE* 5.1 8.3 - - - -
206H VAL* 1.3 93.7 - - - +
208H SER* 1.3 60.6 + - - +
138I ASN* 5.1 11.9 + - - +
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Residues in contact with SER 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H ILE* 3.8 12.1 - - - +
191H SER* 5.7 2.9 - - - -
192H TYR 2.7 21.1 - - - -
193H THR* 3.0 27.3 + - - +
206H VAL* 5.2 2.3 - - - +
207H LYS* 1.3 71.9 - - - +
209H PHE* 1.3 61.0 + - - +
134I ALA 5.2 3.5 - - - +
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Residues in contact with PHE 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H ILE* 3.9 19.1 - - + -
119H PRO* 3.3 39.3 - - + -
120H PRO* 4.5 1.6 - - + -
132H VAL* 3.7 22.0 - - + -
186H TYR* 3.3 22.4 - - - -
191H SER* 3.4 3.7 - - - -
192H TYR* 2.9 72.0 + + + +
208H SER* 1.3 77.0 - - - +
210H ASN* 1.3 63.8 + - - +
211H ARG* 3.9 11.9 - - - -
214H CYS* 5.7 4.5 - - - -
132I GLY* 6.5 0.9 - - - -
134I ALA* 4.9 18.4 - - + +
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Residues in contact with ASN 210 (chain H).
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 4.4 14.6 + - - -
32A LYS* 4.6 11.8 + - - +
35A PRO* 5.1 5.3 - - - +
190H ASN* 3.7 3.6 - - - +
191H SER* 3.6 22.8 - - - +
209H PHE* 1.3 76.8 - - - +
211H ARG* 1.3 66.4 + - - +
212H ASN* 2.8 43.7 + - - +
213H GLU* 2.8 42.4 + - + +
214H CYS* 3.4 8.8 + - - -
134I ALA* 5.2 4.8 - - - +
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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