Contacts of the strand formed by residues 142 - 151 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C ASP* 3.9 40.2 - - + +
212C LEU* 3.7 37.5 - - + -
243C PRO* 4.5 6.3 - - + -
135D VAL 3.5 7.2 - - - +
136D VAL* 4.5 7.4 - - + -
140D GLY 3.7 13.0 - - - +
141D LYS* 1.3 72.3 - - - +
143D PHE* 1.3 69.8 + - - +
144D LYS* 4.1 14.1 - - + +
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Residues in contact with PHE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO 3.9 11.4 - - - -
39D VAL* 4.2 5.6 - - + -
40D ILE* 2.8 71.8 - - + +
42D ALA* 4.6 5.2 - - + +
135D VAL* 2.8 41.3 + - + +
137D ALA* 4.1 7.4 - - + -
141D LYS* 3.5 39.0 - - + -
142D VAL* 1.3 77.4 - - - +
144D LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ASP 2.9 23.8 + - - +
211C GLY* 3.7 4.3 + - - +
42D ALA* 4.4 10.0 - - - +
132D SER* 4.4 2.7 - - - +
133D LEU 3.2 11.9 - - - +
134D GLN* 4.0 25.8 - - + +
142D VAL* 4.1 12.6 - - + -
143D PHE* 1.3 80.7 - - - +
145D ALA* 1.3 63.6 + - - +
146D ASN* 4.2 15.3 - - - +
246D GLU* 2.8 37.0 + - - -
1272D O4B 6.1 0.2 - - - -
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Residues in contact with ALA 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 3.5 26.4 - - + +
43D ASN* 3.7 23.8 - - - -
44D LEU* 3.3 12.5 - - + +
133D LEU* 2.8 38.5 + - + -
144D LYS* 1.3 73.4 - - - +
146D ASN* 1.3 62.6 + - - +
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 3.8 19.4 - - + +
131D VAL 3.2 8.7 - - - +
132D SER* 3.0 29.5 + - - -
144D LYS* 4.2 13.9 - - - +
145D ALA* 1.3 84.6 + - - +
147D GLN* 1.3 77.4 + - - +
148D GLU* 6.0 0.9 - - + -
1272D O4B 5.0 8.1 - - - +
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Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.0 40.2 - - + +
45D SER* 4.1 4.7 - - - -
46D LEU* 3.6 33.2 - - + +
49D ASN* 5.4 5.1 - - - +
130D THR* 3.6 2.8 - - - +
131D VAL* 2.7 39.3 + - - +
146D ASN* 1.3 83.0 + - - +
148D GLU* 1.3 67.6 + - - +
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Residues in contact with GLU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.6 5.3 - - - +
49D ASN* 3.5 20.4 + - - -
128D LYS* 6.2 4.7 - - + -
129D TYR 3.3 11.4 - - - +
130D THR* 4.6 13.9 + - + +
146D ASN* 6.0 0.7 - - + -
147D GLN* 1.3 82.0 + - - +
149D PHE* 1.3 67.2 + - - +
150D VAL* 6.3 0.2 - - + -
155D LEU* 5.0 16.6 - - + +
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.1 6.5 - - + -
49D ASN* 3.2 24.7 - - - +
51D LEU* 4.0 12.6 - - + -
58D ILE* 3.7 23.1 - - + -
80D ILE* 4.2 8.3 - - + -
118D PHE* 4.2 4.9 - + - -
120D VAL* 3.8 22.2 - - + -
128D LYS* 3.9 0.5 - - - +
129D TYR* 2.8 75.7 + + + +
131D VAL* 3.3 35.0 - - + -
148D GLU* 1.3 77.4 - - - +
150D VAL* 1.3 79.3 + - - +
151D LYS* 5.0 0.2 - - + -
155D LEU* 5.5 2.2 - - - -
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Residues in contact with VAL 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN 2.8 17.7 + - - +
50D GLN* 3.8 10.3 - - - +
51D LEU* 2.9 29.2 + - - +
127D GLY 3.4 6.7 - - - +
128D LYS* 4.3 11.7 - - + -
148D GLU* 6.3 0.2 - - + -
149D PHE* 1.3 84.6 - - - +
151D LYS* 1.3 61.2 + - - +
153D VAL* 3.1 35.7 - - + +
154D ASP 4.0 13.2 - - - +
155D LEU* 3.7 31.2 - - + +
156D ASN 4.8 2.0 - - - +
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Residues in contact with LYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 3.3 11.7 - - + -
52D ALA 3.7 9.0 - - - +
53D SER 2.9 26.9 + - - -
55D GLY* 3.7 13.5 - - - -
120D VAL* 3.9 18.6 - - + -
121D PRO 3.4 21.1 - - - -
122D GLU 3.1 6.9 + - - -
124D MET* 2.7 23.8 + - + +
125D ALA 3.9 9.9 - - - +
126D ASP* 3.1 20.7 + - - +
127D GLY 2.8 33.6 + - - +
129D TYR* 4.0 18.6 - - + +
149D PHE* 5.0 0.7 - - + -
150D VAL* 1.3 75.6 - - - +
152D GLY* 1.3 61.4 + - - +
153D VAL 3.2 3.9 + - - -
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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