Contacts of the strand formed by residues 142 - 151 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135E VAL 3.5 7.9 - - - +
136E VAL* 4.5 7.6 - - + -
140E GLY 3.7 13.5 - - - +
141E LYS* 1.3 73.3 - - - +
143E PHE* 1.3 68.6 + - - +
144E LYS* 4.1 14.3 - - + +
210F ASP* 3.9 40.2 - - + +
212F LEU* 3.7 37.7 - - + -
243F PRO* 4.5 4.9 - - + -
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Residues in contact with PHE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 3.8 16.8 - - + -
40E ILE* 3.2 63.3 - - + +
42E ALA* 4.6 8.3 - - + +
135E VAL* 2.8 52.7 + - + +
137E ALA* 4.1 6.5 - - + -
141E LYS* 3.5 39.5 - - + -
142E VAL* 1.3 77.0 - - - +
144E LYS* 1.3 66.3 + - - +
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Residues in contact with LYS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 4.4 10.3 - - - +
132E SER* 4.4 2.5 - - - +
133E LEU 3.2 11.4 - - - +
134E GLN* 4.0 26.9 - - + +
142E VAL* 4.1 12.3 - - + +
143E PHE* 1.3 82.6 - - - +
145E ALA* 1.3 62.9 + - - +
146E ASN* 4.2 13.7 - - - +
246E GLU* 2.8 36.6 + - - -
210F ASP 2.9 24.0 + - - +
211F GLY* 3.7 3.7 - - - +
212F LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 3.5 26.0 - - + +
43E ASN* 3.7 23.8 - - - -
44E LEU* 3.3 12.1 - - + +
133E LEU* 2.8 38.0 + - + -
144E LYS* 1.3 75.0 - - - +
146E ASN* 1.3 62.7 + - - +
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Residues in contact with ASN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E THR* 3.8 19.4 - - + +
131E VAL 3.2 8.1 - - - +
132E SER* 3.0 30.1 + - - -
144E LYS* 4.2 14.4 - - - +
145E ALA* 1.3 84.8 + - - +
147E GLN* 1.3 79.1 + - - +
148E GLU* 6.0 0.9 - - + -
1272E O4B 5.1 9.7 - - - +
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Residues in contact with GLN 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.0 39.4 - - + +
45E SER* 4.1 4.3 - - - -
46E LEU* 3.6 35.0 - - + +
49E ASN* 5.4 5.1 - - - +
130E THR* 3.6 3.3 - - - +
131E VAL* 2.7 39.7 + - - +
146E ASN* 1.3 83.4 + - - +
148E GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 3.6 5.6 - - - +
49E ASN* 3.5 19.9 + - - -
128E LYS* 3.9 27.5 - - + +
129E TYR 3.3 11.0 - - - +
130E THR* 4.6 13.5 + - + +
146E ASN* 6.3 0.7 - - + -
147E GLN* 1.3 82.7 + - - +
149E PHE* 1.3 67.1 + - - +
150E VAL* 6.4 0.2 - - + -
155E LEU* 5.0 16.8 - - + +
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Residues in contact with PHE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 4.1 6.3 - - + -
49E ASN* 3.2 24.0 - - - +
51E LEU* 4.0 13.5 - - + -
58E ILE* 3.7 23.1 - - + -
80E ILE* 4.2 7.0 - - + -
118E PHE* 4.2 6.5 - + - -
120E VAL* 3.8 22.7 - - + -
128E LYS* 3.9 1.6 - - - +
129E TYR* 2.8 76.2 + + + +
131E VAL* 3.3 35.0 - - + -
148E GLU* 1.3 77.6 - - - +
150E VAL* 1.3 77.4 + - - +
151E LYS* 5.0 0.4 - - + -
155E LEU* 5.5 1.8 - - - -
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Residues in contact with VAL 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ASN 2.8 16.9 + - - +
50E GLN* 3.9 10.1 - - + +
51E LEU* 2.9 29.4 + - - +
127E GLY 3.4 7.2 - - - +
128E LYS* 4.3 14.8 - - + -
148E GLU* 6.4 0.2 - - + -
149E PHE* 1.3 85.3 - - - +
151E LYS* 1.3 61.7 + - - +
153E VAL* 3.1 36.6 - - + +
154E ASP 4.0 12.8 - - - +
155E LEU* 3.7 30.3 - - + +
156E ASN 4.8 1.8 - - - +
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Residues in contact with LYS 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.3 10.1 - - + +
52E ALA 3.7 8.5 - - - +
53E SER 2.9 26.5 + - - -
55E GLY* 3.7 13.9 - - - -
120E VAL* 3.9 19.5 - - + -
121E PRO 3.4 21.1 - - - -
122E GLU 3.1 6.9 + - - -
124E MET 2.7 23.9 + - - +
125E ALA 3.9 9.6 - - - +
126E ASP* 3.1 20.6 + - - +
127E GLY 2.8 34.7 + - - +
129E TYR* 4.0 17.5 - - + +
149E PHE* 5.0 1.1 - - + -
150E VAL* 1.3 75.5 - - - +
152E GLY* 1.3 60.4 + - - +
153E VAL 3.2 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
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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