Contacts of the strand formed by residues 131 - 138 (chain A) 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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A HIS* 3.7 10.8 + - - -
112A ARG 3.9 3.4 - - - -
113A PHE* 3.0 28.4 - - - +
114A SER* 2.7 22.7 + - - -
130A ARG* 1.3 74.7 - - - +
132A PHE* 1.3 59.0 + - - +
133A ALA 3.8 2.2 - - - -
147A GLY 3.7 2.5 - - - -
148A ASN* 3.8 1.1 - - - -
600A HEM 3.4 22.9 - - - -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.8 18.2 - - + -
112A ARG 3.8 2.2 - - - -
113A PHE* 3.4 32.1 - + + -
130A ARG 3.6 1.1 + - - +
131A GLY* 1.3 72.0 - - - +
133A ALA* 1.3 57.6 + - - +
134A VAL* 4.0 7.9 - - + -
147A GLY 2.7 19.6 + - - +
148A ASN* 4.0 13.0 - - - -
149A ASN 4.6 0.4 - - - +
212A MET* 4.4 7.4 - - + -
213A ASN 3.9 5.6 - - - -
214A GLY* 3.4 22.4 - - - -
236A TYR* 3.0 50.4 + + + -
277A TRP* 3.3 48.5 - + - -
316A LEU* 5.0 2.5 - - + -
318A LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 3.2 10.2 - - - +
112A ARG 3.1 32.0 + - - +
132A PHE* 1.3 74.8 - - - +
134A VAL* 1.3 60.8 + - - +
145A LEU 3.7 4.9 - - - -
146A VAL* 4.1 10.8 - - + +
147A GLY 4.3 0.2 - - - +
334A PHE* 3.4 37.8 - - + -
600A HEM 4.1 18.4 - - + +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 4.2 15.0 - - + -
110A ALA 3.5 2.5 - - - +
111A VAL* 3.9 19.7 - - + -
132A PHE* 4.0 17.9 - - + -
133A ALA* 1.3 79.6 - - - +
135A LYS* 1.3 62.7 + - - +
136A PHE* 3.3 35.6 - - + -
143A TRP 3.7 1.0 - - - +
144A ASP* 3.6 1.4 - - - -
145A LEU* 2.8 41.9 + - + +
236A TYR* 4.0 20.4 - - + +
316A LEU* 4.3 9.4 - - + -
334A PHE* 3.7 3.9 - - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PRO 3.8 0.2 - - - +
109A ILE* 3.0 8.8 - - - +
110A ALA* 2.8 37.5 + - + +
134A VAL* 1.3 73.0 - - - +
136A PHE* 1.3 62.4 + - - +
137A TYR* 3.4 35.9 + - + +
142A ASN* 3.8 23.4 - - + +
143A TRP 3.6 0.2 - - - -
144A ASP* 3.1 29.9 + - - +
332A ILE* 3.9 17.0 - - - -
333A ALA 3.0 28.2 + - - -
334A PHE* 3.6 8.4 - - + +
338A ASN* 4.9 1.4 - - - +
371A LEU* 6.1 0.6 - - - +
375A VAL 3.5 14.8 - - - +
376A ASN* 4.2 6.0 + - - +
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.6 39.5 - + + -
99A VAL* 4.3 3.8 - - + -
107A THR* 4.1 4.3 - - + -
108A PRO 3.8 3.8 - - - -
109A ILE* 3.8 12.1 - - + -
134A VAL* 3.3 32.1 - - + -
135A LYS* 1.3 72.3 - - - +
137A TYR* 1.3 62.4 + - - +
138A THR* 3.0 15.1 + - + +
142A ASN* 3.4 1.9 - - - -
143A TRP* 2.8 91.2 + + + +
145A LEU* 4.0 14.1 - - + -
279A PHE* 4.3 13.0 - + - -
316A LEU* 3.9 11.9 - - + -
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 4.1 9.4 - + - -
107A THR* 3.3 6.9 - - - +
108A PRO* 3.0 36.8 + - + +
109A ILE 3.8 3.6 - - - -
110A ALA* 3.2 38.3 - - + +
135A LYS* 3.4 22.4 - - + -
136A PHE* 1.3 69.8 - - - +
138A THR* 1.3 58.9 + - - +
142A ASN* 3.5 20.0 - - - +
374A PRO 5.0 0.7 - - - -
375A VAL* 2.8 31.2 + - - +
377A CYS 3.8 10.1 - - - -
379A TYR* 3.4 39.9 - + + -
380A ARG* 3.0 34.1 + - + +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.0 30.5 - - + -
107A THR* 4.2 4.3 - - + -
136A PHE* 3.0 25.3 + - + +
137A TYR* 1.3 75.0 - - - +
139A GLU* 1.3 66.5 + - - +
140A ASP* 2.8 19.6 + - - +
141A GLY* 2.6 39.7 + - - +
142A ASN* 5.0 0.7 - - - +
143A TRP* 4.1 10.5 - - + -
340A PRO* 4.4 4.8 - - + +
378A PRO 5.8 0.2 - - - -
380A ARG* 3.9 8.1 + - - +
381A ALA* 3.7 6.8 - - - +
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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