Contacts of the strand formed by residues 142 - 151 (chain F) in PDB entry 4BEI
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 VAL 142 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E ASP* 3.7 42.0 - - + +
212E LEU* 3.6 31.6 - - + -
243E PRO* 4.2 14.8 - - + -
135F VAL 3.5 6.5 - - - +
136F VAL* 4.4 6.5 - - + -
140F GLY 3.4 14.3 + - - +
141F LYS* 1.3 72.5 - - - +
143F PHE* 1.3 69.2 + - - +
144F LYS* 4.1 13.0 - - + +
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Residues in contact with PHE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 3.8 17.3 - - + -
40F ILE* 3.2 68.2 - - + +
42F ALA* 4.6 8.3 - - + +
134F GLN* 3.6 0.2 - - - -
135F VAL* 2.8 48.4 + - + +
137F ALA* 4.1 6.3 - - + -
141F LYS* 3.5 38.4 - - + -
142F VAL* 1.3 78.7 - - - +
144F LYS* 1.3 66.0 + - - +
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Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ASP* 2.8 24.2 + - - +
211E GLY* 3.6 3.4 + - - +
212E LEU* 5.0 0.2 - - + -
42F ALA* 4.4 9.9 - - - +
132F SER* 4.3 2.0 - - - +
133F LEU 3.2 10.1 - - - +
134F GLN* 4.0 27.8 - - + +
142F VAL* 4.1 11.9 - - + -
143F PHE* 1.3 83.1 - - - +
145F ALA* 1.3 63.4 + - - +
146F ASN* 4.1 14.1 - - - +
246F GLU* 2.7 37.2 + - - -
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Residues in contact with ALA 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F ALA* 3.5 25.8 - - + +
43F ASN* 3.7 18.4 - - - -
44F LEU* 3.3 17.2 - - + +
133F LEU* 2.8 37.6 + - + -
144F LYS* 1.3 74.9 - - - +
146F ASN* 1.3 62.6 + - - +
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Residues in contact with ASN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 4.4 0.4 - - - -
130F THR* 3.8 20.0 - - + +
131F VAL 3.2 8.1 - - - +
132F SER* 3.1 30.4 + - - -
144F LYS* 4.1 12.7 - - - +
145F ALA* 1.3 85.3 + - - +
147F GLN* 1.3 78.5 + - - +
148F GLU* 6.0 0.9 - - + -
1272F O4B 5.2 7.3 - - - +
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Residues in contact with GLN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.0 39.3 - - + +
45F SER* 4.1 4.9 - - - -
46F LEU* 3.6 35.2 - - + +
49F ASN* 5.4 5.1 - - - +
130F THR* 3.6 3.7 - - - +
131F VAL* 2.7 39.4 + - + +
146F ASN* 1.3 83.9 + - - +
148F GLU* 1.3 66.3 + - - +
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Residues in contact with GLU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 3.6 5.1 - - - +
49F ASN* 3.6 19.8 + - - +
128F LYS* 4.7 16.9 - - + +
129F TYR 3.3 12.1 - - - +
130F THR* 4.6 13.6 + - + +
146F ASN* 6.3 0.7 - - + -
147F GLN* 1.3 82.3 + - - +
149F PHE* 1.3 65.6 - - - +
155F LEU* 4.9 11.7 - - + +
156F ASN* 4.4 15.8 + - - -
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Residues in contact with PHE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 4.2 6.3 - - + -
49F ASN* 3.2 24.5 - - - +
51F LEU* 4.0 11.9 - - + -
58F ILE* 3.8 22.9 - - + -
80F ILE* 4.2 8.5 - - + -
118F PHE* 4.2 5.2 - + - -
120F VAL* 3.9 22.7 - - + -
128F LYS* 3.9 1.4 - - - +
129F TYR* 2.8 75.7 + + + +
131F VAL* 3.3 34.8 - - + -
148F GLU* 1.3 77.3 - - - +
150F VAL* 1.3 78.9 + - - +
151F LYS* 5.0 0.7 - - + -
155F LEU* 5.5 1.8 - - - -
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ASN 2.8 17.8 + - - +
50F GLN* 4.0 10.1 - - + -
51F LEU* 2.9 28.7 + - - +
127F GLY 3.4 7.4 - - - +
128F LYS* 4.3 15.0 - - + -
149F PHE* 1.3 84.5 - - - +
151F LYS* 1.3 61.9 + - - +
153F VAL* 3.1 36.1 - - + +
154F ASP 4.0 13.0 - - - +
155F LEU* 3.6 30.7 - - + +
156F ASN 4.7 2.0 - - - +
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Residues in contact with LYS 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F LEU* 3.3 10.8 - - + +
52F ALA 3.7 8.7 - - - +
53F SER 2.9 27.0 + - - -
55F GLY* 3.7 14.1 - - - -
120F VAL* 3.9 20.2 - - + -
121F PRO 3.4 21.1 - - - -
122F GLU 3.1 6.9 + - - -
124F MET* 2.7 23.5 + - + +
125F ALA 3.9 9.6 - - - +
126F ASP* 3.1 21.2 + - - +
127F GLY* 2.8 33.7 + - - +
129F TYR* 4.0 18.2 - - + +
149F PHE* 5.0 0.9 - - + -
150F VAL* 1.3 76.1 - - - +
152F GLY* 1.3 61.8 + - - +
153F VAL 3.3 3.4 + - - -
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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