Contacts of the strand formed by residues 143 - 148 (chain I) in PDB entry 3FFC
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 SER 143 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133I GLN* 3.5 21.3 + - - -
134I LEU 4.7 2.2 + - - -
136I ASP* 4.2 9.1 + - - -
142I LYS* 1.3 76.4 + - - +
144I VAL* 1.3 62.6 + - - +
187I TRP* 3.4 19.8 - - - -
188I SER 3.5 9.4 + - - -
193I PHE* 3.7 22.2 - - - -
144J PHE* 4.8 0.2 - - - -
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Residues in contact with VAL 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I GLN* 4.1 2.7 + - - +
134I LEU* 3.0 39.9 + - + +
142I LYS* 5.2 0.2 - - + -
143I SER* 1.3 72.7 + - - +
145I CYS* 1.3 66.4 + - - +
146I LEU 4.8 0.2 - - - +
185I VAL* 3.6 25.8 - - + -
186I ALA 3.5 2.0 - - - -
187I TRP* 3.8 19.1 - - + -
144J PHE* 3.6 42.9 - - + -
160J VAL* 3.9 21.5 - - + -
162J LEU* 3.9 11.4 - - + -
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Residues in contact with CYS 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I VAL* 4.6 0.9 - - + -
132I TYR 3.6 3.8 - - - +
133I GLN* 4.5 3.1 - - - -
143I SER 3.9 0.4 + - - -
144I VAL* 1.3 75.3 - - - +
146I LEU* 1.3 60.7 + - - +
147I PHE 3.9 1.1 + - - -
185I VAL* 3.4 5.9 - - - +
186I ALA* 2.8 41.4 + - + +
193I PHE* 3.6 24.2 - - + -
195I CYS* 2.1 56.5 - - + -
198I ALA* 4.5 2.7 - - + -
199I PHE* 4.3 17.7 - - + -
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Residues in contact with LEU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ALA 3.5 0.3 - - - +
131I VAL* 4.2 1.8 - - - -
132I TYR* 3.0 34.6 + - + +
134I LEU* 3.9 26.7 - - + -
144I VAL* 4.1 0.8 + - + -
145I CYS* 1.3 73.2 - - - +
147I PHE* 1.3 58.7 + - - +
148I THR* 3.4 33.8 + - + +
183I SER* 4.3 5.2 - - - -
184I ALA 3.5 14.4 - - - +
185I VAL* 3.9 15.7 - - + -
150J GLU* 4.0 6.1 - - - +
158J THR* 3.7 31.9 - - + +
160J VAL* 4.2 9.9 - - + -
209J ARG* 4.0 16.6 - - + -
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Residues in contact with PHE 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I PRO* 4.8 1.1 - - + -
130I ALA 3.3 7.6 - - - -
131I VAL* 3.5 21.1 - - + +
146I LEU* 1.3 69.3 - - - +
148I THR* 1.3 60.6 + - - +
150I PHE* 3.3 54.0 - + + -
154I THR* 4.3 7.0 - - + -
156I VAL* 4.4 12.1 - - + -
184I ALA* 2.8 42.4 + - + +
199I PHE* 3.3 41.5 - + + -
202I SER* 6.2 0.7 - - - -
204I ILE* 3.6 30.5 - - + -
205I PRO* 4.2 9.4 - - + -
208I THR* 4.0 15.9 - - + -
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Residues in contact with THR 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I PRO* 3.8 0.3 - - - +
130I ALA* 2.7 33.3 + - + +
132I TYR* 3.4 39.9 - - + -
146I LEU* 3.8 22.9 - - + +
147I PHE* 1.3 75.1 - - - +
149I ASP* 1.3 71.6 + - + +
150I PHE* 2.9 21.3 + - - +
172I LEU* 5.6 0.5 - - - +
181I SER* 3.7 9.5 + - - -
182I ASN 3.2 13.9 + - - -
183I SER* 4.2 4.1 - - - -
158J THR* 5.2 1.2 + - - -
211J ARG* 4.4 8.1 + - - +
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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