Contacts of the strand formed by residues 137 - 143 (chain L) 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 ASP 137 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163G LYS* 5.3 0.2 - - - -
164G TYR 5.0 2.3 + - - +
167G GLY* 3.7 10.0 - - - -
168G ASN* 2.7 38.8 + - - +
135L PHE* 3.6 4.9 - - - +
136L ASP* 1.3 83.0 - - + +
138L ILE* 1.3 62.4 + - - +
139L ARG* 2.6 36.2 + - - +
150L ALA 4.6 1.9 - - - +
151L ILE* 3.7 1.6 - - - -
152L ASP* 2.9 48.2 + - + +
252L THR* 4.7 0.2 - - - -
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Residues in contact with ILE 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462F PHE* 4.4 8.1 - - + -
466F TYR* 3.6 49.6 - - + +
160G SER 3.9 1.7 - - - +
168G ASN* 2.9 36.0 + - - +
169G LYS 4.0 2.2 - - - -
170G GLY* 3.9 19.6 - - - +
135L PHE* 5.0 2.7 - - + -
137L ASP* 1.3 75.5 - - - +
139L ARG* 1.3 68.3 + - - +
140L PHE* 4.0 13.6 - - + -
149L VAL* 4.3 9.2 - - + -
150L ALA 3.4 16.2 - - - +
151L ILE* 4.0 21.8 - - + -
252L THR* 4.0 2.9 - - + +
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Residues in contact with ARG 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G SER 3.2 8.3 - - - +
161G SER* 3.5 14.3 + - - +
162G THR 3.5 20.4 - - - +
163G LYS* 3.5 41.7 - - - +
168G ASN* 3.8 6.7 - - + +
137L ASP* 2.6 42.6 + - - +
138L ILE* 1.3 80.1 - - - +
140L PHE* 1.3 66.7 + - - +
148L HIS* 4.4 8.0 + - + +
149L VAL* 3.2 1.9 - - - +
150L ALA* 2.6 62.5 + - + +
152L ASP* 5.8 0.2 - - - +
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Residues in contact with PHE 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F PRO 4.5 3.1 - - - +
462F PHE* 3.6 37.7 - - + -
463F GLU* 3.4 36.3 - - + -
466F TYR* 4.5 10.1 - + + -
160G SER* 2.9 55.6 + - - -
161G SER* 3.3 2.9 + - - -
170G GLY* 4.9 14.4 - - - -
138L ILE* 4.0 22.7 - - + -
139L ARG* 1.3 79.6 - - - +
141L GLY* 1.3 62.5 + - - +
148L HIS* 3.0 27.5 + - - +
149L VAL* 3.9 6.1 - - + -
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Residues in contact with GLY 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F PRO* 4.3 3.7 + - - +
463F GLU* 4.7 4.7 - - - -
160G SER* 4.5 4.7 - - - -
161G SER* 4.9 2.7 - - - -
140L PHE* 1.3 81.8 - - - +
142L ALA* 1.3 61.8 + - - -
147L SER* 3.0 4.8 - - - -
148L HIS* 2.8 45.4 + - - +
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Residues in contact with ALA 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460F VAL* 4.1 19.7 - - + +
463F GLU* 4.0 18.6 + - - +
141L GLY* 1.3 75.6 - - - +
143L SER* 1.3 63.2 + - - +
146L GLY 3.5 5.6 - - - +
147L SER* 3.8 12.3 - - - -
452L ARG* 4.6 6.9 + - - +
456L THR* 4.8 5.6 - - + +
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Residues in contact with SER 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TRP* 6.1 0.2 - - - +
261F PHE* 5.5 7.5 - - - +
142L ALA* 1.3 77.4 - - - +
144L ILE* 1.3 70.6 + - - +
145L SER* 3.0 23.4 + - - -
146L GLY* 2.7 20.8 + - - +
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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