Contacts of the strand formed by residues 131 - 138 (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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B HIS* 3.6 19.9 - - - -
112B ARG 4.0 4.5 - - - -
113B PHE* 3.3 9.9 - - - -
114B SER* 2.9 40.6 + - - -
130B ARG* 1.3 75.7 - - - +
132B PHE* 1.3 59.0 + - - +
133B ALA 4.0 1.6 - - - -
147B GLY 3.9 2.0 - - - -
148B ASN* 4.1 0.9 - - - -
212B MET* 3.9 3.5 - - - +
600B HEM 3.7 7.4 - - - -
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Residues in contact with PHE 132 (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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111B VAL* 3.9 13.5 - - + -
112B ARG 3.8 3.1 - - - -
113B PHE* 3.3 37.0 - + - -
130B ARG 3.7 0.2 + - - -
131B GLY* 1.3 72.6 - - - +
133B ALA* 1.3 59.8 + - - +
134B VAL* 3.9 11.7 - - + -
147B GLY 2.7 20.5 + - - +
148B ASN* 4.1 11.7 - - - -
209B HIS 4.8 0.2 - - - -
212B MET* 3.7 17.3 - - + -
213B ASN 4.1 2.7 - - - -
214B GLY* 4.0 11.0 - - - -
236B TYR* 2.9 52.2 + + + +
277B TRP* 3.5 46.0 - + - -
316B LEU* 5.2 1.8 - - + -
600B HEM 4.0 0.2 - - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA 3.8 0.2 - - - +
111B VAL* 3.2 8.3 - - - +
112B ARG* 3.1 33.8 + - + +
131B GLY 4.0 0.2 - - - -
132B PHE* 1.3 73.8 - - - +
134B VAL* 1.3 63.3 + - - +
145B LEU 3.7 5.2 - - - -
146B VAL* 4.1 19.7 - - + +
334B PHE* 3.6 39.9 - - + -
600B HEM 4.2 7.0 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.1 18.6 - - + -
110B ALA 3.5 1.6 - - - -
111B VAL* 4.1 15.0 - - + -
132B PHE* 3.9 25.6 - - + -
133B ALA* 1.3 81.5 - - - +
135B LYS* 1.3 61.7 + - - +
136B PHE* 3.6 31.3 - - + -
143B TRP 3.6 3.5 - - - +
144B ASP* 3.6 0.5 - - - -
145B LEU* 2.8 40.2 + - + +
236B TYR* 4.0 18.2 - - + +
316B LEU* 4.3 10.1 - - + -
334B PHE* 3.9 2.9 - - - -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO 3.6 0.7 - - - +
109B ILE* 2.9 9.2 - - - -
110B ALA* 2.7 43.0 + - + +
134B VAL* 1.3 72.5 - - - +
136B PHE* 1.3 61.2 + - - +
137B TYR* 3.6 34.8 + - + +
142B ASN* 3.8 23.3 - - + +
144B ASP* 2.7 36.8 + - - +
332B ILE* 4.0 16.8 - - - -
333B ALA 2.9 27.3 + - - -
334B PHE* 3.5 11.8 - - + -
338B ASN* 4.6 2.2 - - - +
371B LEU* 6.1 1.2 - - - +
375B VAL 3.6 13.7 - - - +
376B ASN* 4.1 6.8 + - - +
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Residues in contact with PHE 136 (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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85B PHE* 3.5 42.8 - + + -
99B VAL* 3.9 9.4 - - + -
107B THR* 4.3 3.6 - - + -
108B PRO 3.6 3.8 - - - -
109B ILE* 4.0 5.2 - - + -
134B VAL* 3.6 30.3 - - + -
135B LYS* 1.3 74.1 - - - +
137B TYR* 1.3 61.6 + - - +
138B THR* 3.1 20.4 + - + +
142B ASN* 3.3 2.8 - - - -
143B TRP* 2.9 89.3 + + + +
145B LEU* 4.2 7.6 - - + -
279B PHE* 4.2 12.6 - + - -
316B LEU* 4.1 10.1 - - + -
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Residues in contact with TYR 137 (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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82B PHE* 4.7 4.6 - + - -
107B THR* 3.4 12.1 - - - +
108B PRO* 3.0 33.1 + - + +
109B ILE 4.2 2.5 - - - -
110B ALA* 3.5 35.6 - - + +
135B LYS* 3.6 15.9 - - + -
136B PHE* 1.3 68.8 - - - +
138B THR* 1.3 59.7 + - - +
142B ASN* 3.5 17.3 - - - +
374B PRO 5.0 0.4 - - - -
375B VAL* 2.7 36.6 + - - +
377B CYS 3.4 25.4 - - - -
379B TYR* 3.4 32.1 - + + -
380B ARG* 3.1 30.0 + - + +
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Residues in contact with THR 138 (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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98B LYS* 5.4 0.7 - - - -
99B VAL* 3.9 33.2 - - + -
107B THR* 4.1 10.1 - - + -
136B PHE* 3.1 25.7 + - + +
137B TYR* 1.3 75.7 - - - +
139B GLU* 1.3 64.0 + - - +
140B ASP* 3.0 18.2 + - - +
141B GLY* 2.5 39.1 + - - +
142B ASN* 4.7 0.9 - - - +
143B TRP* 4.5 7.9 - - + -
340B PRO* 4.5 5.6 - - + +
380B ARG* 3.8 9.9 + - - +
381B ALA* 3.9 4.3 - - - +
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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
------------------------------------------------------------
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