Contacts of the strand formed by residues 146 - 152 (chain C) in PDB entry 1FPY
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 GLY 146 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER* 2.7 36.5 + - - +
144C ILE 3.3 3.6 + - - -
145C SER* 1.3 81.7 + - - +
147C SER* 1.3 63.7 + - - -
149I VAL* 3.2 22.9 - - - -
150I ALA* 4.6 0.4 - - - -
151I ILE* 5.1 1.1 - - - -
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Residues in contact with SER 147 (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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141C GLY 3.0 15.5 - - - -
142C ALA* 3.8 13.0 - - - -
146C GLY* 1.3 75.1 - - - -
148C HIS* 1.3 69.0 + - - +
456C THR* 4.9 7.4 - - - -
457C PRO 3.9 15.1 + - - -
459C PRO* 4.1 1.6 - - - +
148I HIS* 3.2 1.0 - - - -
149I VAL* 2.9 41.9 + - - +
458I HIS* 4.7 0.5 + - - -
459I PRO* 3.8 19.1 - - - +
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Residues in contact with HIS 148 (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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161B SER* 3.8 29.1 + - - -
139C ARG* 4.3 8.1 + - + +
140C PHE* 3.0 21.0 + - - +
141C GLY* 2.8 53.7 + - - -
147C SER* 1.3 79.7 - - - +
149C VAL* 1.3 68.9 + - - +
150C ALA* 4.8 4.0 - - + -
147I SER 3.3 7.2 - - - +
148I HIS* 3.3 19.7 - - + -
149I VAL 5.5 0.2 - - - +
459I PRO* 3.4 13.7 - - - +
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE* 4.3 6.5 - - + -
139C ARG 3.2 10.1 - - - +
140C PHE* 4.1 2.7 - - + -
148C HIS* 1.3 80.5 - - - +
150C ALA* 1.3 67.4 + - - +
151C ILE* 4.5 5.4 - - + -
146I GLY* 3.2 8.9 - - - -
147I SER* 2.9 43.8 + - - +
148I HIS* 5.5 0.2 - - - +
457I PRO* 5.3 1.8 - - + +
459I PRO* 4.1 7.4 - - + -
462I PHE* 3.4 55.9 - - + -
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Residues in contact with ALA 150 (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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137C ASP* 3.8 2.4 - - - +
138C ILE* 3.4 6.8 - - - +
139C ARG* 2.6 70.4 + - + +
148C HIS* 5.2 4.5 - - + -
149C VAL* 1.3 77.1 - - - +
151C ILE* 1.3 65.2 + - - +
145I SER 3.7 2.7 - - - -
146I GLY* 4.6 0.4 - - - -
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Residues in contact with ILE 151 (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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135C PHE* 3.6 41.3 - - + -
137C ASP* 3.7 2.7 - - - +
138C ILE* 4.0 12.8 - - + -
149C VAL* 4.5 5.8 - - + -
150C ALA* 1.3 78.8 - - - +
152C ASP* 1.3 71.9 + - - +
158C TRP* 3.7 11.6 + - + -
259C PRO* 3.8 26.9 - - + +
260C MET* 3.5 27.8 - - + -
145I SER* 2.7 41.7 + - - +
146I GLY* 5.5 0.9 - - - -
462I PHE* 4.4 7.0 - - + -
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Residues in contact with ASP 152 (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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135C PHE* 3.4 4.5 - - - +
136C ASP* 2.8 31.8 + - + -
137C ASP* 2.9 38.5 + - + +
139C ARG* 5.8 0.4 - - - +
151C ILE* 1.3 78.5 - - - +
153C ASP* 1.3 58.7 + - - +
158C TRP* 3.0 16.5 + - - -
159C ASN* 2.8 33.9 + - - +
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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