Contacts of the strand formed by residues 141 - 148 (chain B) in PDB entry 1F4J
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B THR* 2.5 42.6 + - - +
139B GLU 3.1 3.2 + - - -
140B ASP* 1.3 78.3 - - - +
142B ASN* 1.3 66.4 + - - -
340B PRO* 4.9 0.7 - - - +
381B ALA* 3.7 6.8 - - - +
31D ALA 3.3 6.5 - - - -
32D GLY* 3.0 19.9 + - - -
33D ASN* 3.2 6.3 - - - -
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LYS* 3.8 22.3 - - + +
136B PHE 3.3 6.3 - - - +
137B TYR* 3.5 27.7 - - - +
138B THR 4.7 0.7 - - - +
141B GLY* 1.3 74.3 - - - -
143B TRP* 1.3 60.3 + - - +
144B ASP 4.0 0.9 - - - -
338B ASN* 3.6 28.1 - - - +
339B MET 4.2 0.2 + - - -
340B PRO* 4.3 0.9 - - - +
371B LEU* 6.1 0.2 - - - +
376B ASN 3.6 22.0 + - - -
377B CYS 3.6 10.5 + - - -
378B PRO* 3.1 23.6 - - - +
31D ALA* 3.0 14.1 + - + +
33D ASN* 3.3 15.6 + - - -
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 4.1 11.7 - - + -
100B PHE* 3.8 30.5 - + - -
136B PHE* 2.9 90.4 + + + +
138B THR* 4.5 3.6 - - + -
142B ASN* 1.3 73.4 - - - +
144B ASP* 1.3 70.3 + - - +
145B LEU* 4.2 19.7 - - + +
220B PHE* 6.1 1.4 - - - -
234B PHE* 3.8 26.9 - + - -
279B PHE* 3.9 20.0 - + - -
338B ASN 3.3 14.8 - - - -
339B MET* 4.3 7.1 - - + +
340B PRO* 3.6 26.2 - - + -
343B ILE* 3.6 22.4 - - + +
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Residues in contact with ASP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL 3.6 2.0 - - - -
135B LYS* 2.7 49.6 + - - +
142B ASN* 5.2 0.9 - - - -
143B TRP* 1.3 78.6 + - - +
145B LEU* 1.3 61.4 + - - +
146B VAL* 3.6 3.3 + - + -
220B PHE* 6.2 0.3 - - - -
333B ALA 3.8 0.2 - - - +
334B PHE* 3.4 13.9 - - + -
335B ASP 2.9 37.3 + - - +
336B PRO* 4.0 10.4 - - - +
338B ASN* 2.6 41.6 + - - +
339B MET* 5.3 0.3 - - - +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE 3.9 1.7 - - - +
133B ALA* 3.7 0.2 - - - -
134B VAL* 2.8 36.5 + - + +
136B PHE* 4.2 12.8 - - + -
143B TRP* 3.7 16.1 + - + +
144B ASP* 1.3 71.4 - - - +
146B VAL* 1.3 59.5 + - - +
147B GLY 3.2 6.1 + - - -
216B GLY* 4.3 11.9 - - - -
220B PHE* 4.1 19.5 - - + -
234B PHE* 3.7 41.7 - - + -
236B TYR* 3.8 31.8 + - + +
279B PHE* 4.0 16.8 - - + -
334B PHE* 5.5 0.2 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA* 4.1 10.1 - - + +
144B ASP* 3.6 6.4 + - + -
145B LEU* 1.3 71.0 - - - +
147B GLY* 1.3 58.1 + - - +
216B GLY* 4.7 2.0 - - - +
220B PHE* 6.3 0.2 - - - -
334B PHE* 3.4 27.4 - - + -
336B PRO* 3.8 31.3 - - + +
354B ARG* 3.1 41.8 + - - +
358B TYR* 4.0 7.2 - - + -
600B HEM 3.5 38.5 - - + +
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE 2.7 38.7 + - - +
145B LEU 3.2 8.3 + - - -
146B VAL* 1.3 77.4 - - - +
148B ASN* 1.3 57.8 + - - +
215B TYR 3.1 17.7 - - - -
216B GLY* 4.3 3.3 - - - -
236B TYR* 4.0 3.1 + - - -
600B HEM 3.7 15.6 - - - +
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Residues in contact with ASN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B HIS* 5.1 3.8 + - + -
129B PRO* 5.0 5.3 - - - +
130B ARG 2.7 26.7 - - - +
131B GLY* 4.1 3.1 - - - -
132B PHE* 3.8 8.1 - - - +
147B GLY* 1.3 73.4 - - - +
149B ASN* 1.3 59.7 + - - +
150B THR* 3.2 27.5 + - + +
152B ILE 4.8 0.4 + - - +
153B PHE* 4.5 10.3 - - - -
213B ASN 4.3 1.1 - - - -
214B GLY* 3.4 2.6 - - - -
215B TYR* 2.9 27.4 + - - +
217B SER* 3.0 23.0 + - - -
600B HEM 2.9 37.6 - - + +
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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