Contacts of the strand formed by residues 137 - 143 (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 ASP 137 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135K PHE* 3.6 4.5 - - - +
136K ASP* 1.3 83.6 - - + +
138K ILE* 1.3 62.4 + - - +
139K ARG* 2.6 36.9 + - - +
150K ALA 4.6 1.4 - - - +
151K ILE* 3.7 1.6 - - - -
152K ASP* 2.9 47.6 + - + +
252K THR* 4.7 0.2 - - - -
164L TYR 4.8 2.1 + - - -
167L GLY* 3.4 13.1 - - - -
168L ASN* 2.6 36.0 + - - +
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Residues in contact with ILE 138 (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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462E PHE* 4.4 8.3 - - + -
466E TYR* 3.5 50.5 - - + +
135K PHE* 5.0 2.9 - - + -
137K ASP* 1.3 74.4 - - - +
139K ARG* 1.3 68.6 + - - +
140K PHE* 4.0 13.7 - - + -
149K VAL* 4.3 9.0 - - + -
150K ALA 3.4 15.7 - - - +
151K ILE* 4.0 21.5 - - + -
252K THR* 4.0 2.7 - - + +
160L SER 4.0 1.7 - - - +
168L ASN* 2.8 38.6 + - - +
169L LYS 3.9 2.2 - - - -
170L GLY* 3.8 18.2 + - - +
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Residues in contact with ARG 139 (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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137K ASP* 2.6 42.1 + - - +
138K ILE* 1.3 79.2 - - - +
140K PHE* 1.3 65.8 + - - +
148K HIS* 4.4 7.3 + - - +
149K VAL* 3.2 2.3 - - - +
150K ALA* 2.6 61.9 + - + +
152K ASP* 5.8 0.4 - - - +
160L SER 3.3 7.9 - - - +
161L SER* 3.6 13.6 + - - +
162L THR 3.4 19.7 - - - +
163L LYS* 3.3 48.6 - - - +
168L ASN* 3.7 7.2 - - + +
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Residues in contact with PHE 140 (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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459E PRO 4.5 3.4 - - - +
462E PHE* 3.6 38.1 - - + -
463E GLU* 3.3 35.9 - - + -
466E TYR* 4.4 9.2 - + + -
467E SER* 6.2 0.2 - - - -
138K ILE* 4.0 22.7 - - + -
139K ARG* 1.3 79.9 - - - +
141K GLY* 1.3 62.0 + - - +
148K HIS* 3.0 27.4 + - - +
149K VAL* 3.9 5.6 - - + -
160L SER* 2.9 61.1 + - - -
161L SER 3.1 2.6 + - - -
170L GLY* 4.7 16.2 - - - -
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Residues in contact with GLY 141 (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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459E PRO* 4.3 3.9 + - - +
463E GLU* 4.6 4.9 - - - -
140K PHE* 1.3 83.1 - - - +
142K ALA* 1.3 60.3 + - - -
147K SER* 3.0 5.5 - - - -
148K HIS* 2.8 43.3 + - - +
160L SER* 4.4 5.4 - - - -
161L SER* 4.7 3.1 - - - -
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Residues in contact with ALA 142 (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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460E VAL* 4.1 19.5 - - + +
463E GLU* 3.9 18.4 + - - +
141K GLY* 1.3 76.3 - - - +
143K SER* 1.3 63.2 + - - +
146K GLY 3.5 5.6 - - - +
147K SER* 3.8 12.6 - - - -
452K ARG* 4.6 6.9 + - - +
456K THR* 4.8 5.8 - - + +
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Residues in contact with SER 143 (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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158E TRP* 6.1 0.2 - - - +
261E PHE* 5.5 7.5 - - - +
142K ALA* 1.3 75.9 - - - +
144K ILE* 1.3 70.4 + - - +
145K SER* 3.0 22.7 + - - -
146K 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