Contacts of the strand formed by residues 146 - 152 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E VAL* 3.3 21.5 - - - -
150E ALA* 4.7 0.7 - - - -
151E ILE* 5.2 1.1 - - - -
143K SER* 2.7 36.8 + - - +
144K ILE 3.3 3.4 + - - -
145K SER* 1.3 82.7 + - - +
147K SER* 1.3 63.5 + - - -
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Residues in contact with SER 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E HIS* 3.3 1.4 - - - -
149E VAL* 3.0 41.3 + - - +
458E HIS* 4.7 0.3 + - - -
459E PRO* 3.8 19.0 - - - +
141K GLY 3.0 15.0 - - - -
142K ALA* 3.8 13.7 - - - +
146K GLY* 1.3 75.8 - - - -
148K HIS* 1.3 67.7 + - - +
456K THR* 4.9 7.9 - - - -
457K PRO 3.9 15.1 + - - -
459K PRO* 4.1 1.7 - - - +
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Residues in contact with HIS 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E SER 3.3 8.1 - - - +
148E HIS* 3.4 18.6 - - + -
459E PRO* 3.5 12.5 - - - +
139K ARG* 4.3 8.3 + - + +
140K PHE* 3.0 23.5 + - - +
141K GLY* 2.8 53.1 + - - -
147K SER* 1.3 79.8 - - - +
149K VAL* 1.3 69.2 + - - +
150K ALA* 4.8 3.8 - - + -
161L SER* 3.8 25.6 + - - -
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Residues in contact with VAL 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E GLY* 3.3 8.4 - - - -
147E SER* 3.0 45.7 + - - +
457E PRO* 5.3 1.1 - - + +
459E PRO* 4.2 6.7 - - + -
462E PHE* 3.5 54.7 - - + -
138K ILE* 4.3 7.0 - - + -
139K ARG 3.2 10.8 - - - +
140K PHE* 3.9 2.9 - - + -
148K HIS* 1.3 79.7 - - - +
150K ALA* 1.3 67.1 + - - +
151K ILE* 4.5 5.8 - - + -
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Residues in contact with ALA 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E SER 3.7 2.9 - - - -
146E GLY* 4.6 0.2 - - - -
137K ASP* 3.8 2.4 - - - +
138K ILE* 3.4 7.7 + - - +
139K ARG* 2.6 69.2 + - + +
148K HIS* 5.2 4.5 - - + -
149K VAL* 1.3 77.5 - - - +
151K ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ILE 4.8 0.2 - - - +
145E SER* 2.7 32.9 + - - +
146E GLY* 5.4 0.7 - - - -
462E PHE* 4.4 7.0 - - + -
135K PHE* 3.6 41.7 - - + -
137K ASP 3.7 3.1 - - - +
138K ILE* 4.0 12.6 - - + -
149K VAL* 4.5 6.1 - - + -
150K ALA* 1.3 78.4 - - - +
152K ASP* 1.3 71.8 + - - +
158K TRP* 3.7 19.2 + - + -
259K PRO* 3.8 26.9 - - + +
260K MET* 3.5 28.0 - - + -
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Residues in contact with ASP 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K PHE* 3.4 4.5 - - - +
136K ASP* 2.8 30.8 + - + -
137K ASP* 2.9 38.2 + - + +
139K ARG* 5.8 0.2 - - - +
151K ILE* 1.3 79.6 - - - +
153K ASP* 1.3 59.1 + - - +
158K TRP* 3.0 16.0 + - - -
159K ASN* 2.8 34.5 + - - +
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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