Contacts of the strand formed by residues 130 - 134 (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 ALA 130 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ASP 3.3 6.0 + - - +
129I PRO* 1.3 75.0 - - - +
131I VAL* 1.3 62.4 + - - +
132I TYR* 3.4 43.3 - - + +
147I PHE* 3.3 4.9 - - - -
148I THR* 2.7 41.3 + - + +
149I ASP* 5.3 0.2 - - + -
208I THR* 4.0 1.5 - - - +
209I PHE* 3.6 17.9 - - + +
153J HIS* 4.8 0.9 - - + -
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Residues in contact with VAL 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I ALA* 1.3 71.1 - - - +
132I TYR* 1.3 63.9 + - - +
133I GLN* 5.6 0.2 - - - +
145I CYS* 4.6 0.9 - - + -
146I LEU 3.4 5.6 - - - +
147I PHE* 3.5 30.3 - - + -
195I CYS* 3.5 39.4 - - + +
199I PHE* 4.0 22.9 - - + -
204I ILE* 5.4 1.8 - - + -
208I THR* 3.9 13.0 - - + -
209I PHE 3.2 7.9 + - - +
210I PHE* 4.0 22.8 - - + -
211I PRO* 3.7 19.3 - - - +
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Residues in contact with TYR 132 (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* 3.4 20.4 - - + +
131I VAL* 1.3 75.1 - - - +
133I GLN* 1.3 61.8 + - - +
134I LEU* 4.0 8.3 - - + -
145I CYS* 3.6 0.2 - - - -
146I LEU* 3.0 32.7 + - + +
148I THR* 3.4 34.1 - - + -
149I ASP* 4.7 0.6 + - - -
195I CYS* 3.3 12.7 - - - -
209I PHE* 4.8 1.1 - + - -
211I PRO* 4.3 13.0 - - + -
147J SER* 3.3 15.7 - - - +
149J ALA* 3.9 15.3 - - + -
150J GLU* 3.4 50.7 - - + -
153J HIS* 2.8 30.9 + + + +
154J THR* 3.4 14.0 + - - +
211J ARG* 4.8 2.0 - - - -
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Residues in contact with GLN 133 (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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132I TYR* 1.3 74.0 - - - +
134I LEU* 1.3 69.5 + - - +
135I ARG* 3.7 1.8 + - - +
143I SER* 3.5 25.1 + - - -
144I VAL 4.1 5.9 + - - -
145I CYS* 4.5 1.1 - - - -
194I ALA* 5.2 2.8 - - - +
195I CYS* 3.4 30.1 + - + +
211I PRO 5.5 6.5 - - - +
212I SER* 5.9 4.3 - - - +
147J SER* 3.0 22.4 - - - -
149J ALA* 5.9 1.0 - - - +
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Residues in contact with LEU 134 (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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132I TYR* 4.2 4.9 - - + -
133I GLN* 1.3 82.1 + - - +
135I ARG* 1.3 66.3 + - - +
136I ASP* 3.9 1.4 + - - +
143I SER* 4.7 2.3 + - - -
144I VAL* 3.0 33.5 + - + +
146I LEU* 3.9 31.4 - - + -
144J PHE* 3.7 17.6 - - + +
145J GLU 3.3 18.4 - - - +
147J SER* 3.7 24.2 - - - +
150J GLU* 4.3 3.6 - - - +
158J THR 3.3 21.5 - - - +
160J VAL* 3.6 28.7 - - + -
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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