Contacts of the strand formed by residues 142 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A VAL 3.5 6.5 - - - +
136A VAL* 4.5 13.9 - - + -
140A GLY 3.5 14.6 + - - +
141A LYS* 1.3 74.5 - - - +
143A PHE* 1.3 69.7 + - - +
144A LYS* 4.1 14.3 - - + +
210B ASP* 3.9 40.8 - - + +
212B LEU* 3.7 31.4 - - + -
243B PRO* 4.5 5.2 - - + -
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Residues in contact with PHE 143 (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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39A VAL* 3.9 17.7 - - + -
40A ILE* 3.2 64.4 - - + +
42A ALA* 4.6 8.3 - - + -
135A VAL* 2.8 50.2 + - + +
137A ALA* 4.1 7.0 - - + -
141A LYS* 3.5 40.6 - - + -
142A VAL* 1.3 78.2 - - - +
144A LYS* 1.3 65.3 + - - +
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Residues in contact with LYS 144 (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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42A ALA* 4.4 10.0 - - - +
132A SER* 4.4 2.2 - - - +
133A LEU 3.2 11.0 - - - +
134A GLN* 4.0 27.6 - - + +
142A VAL* 4.1 11.7 - - + -
143A PHE* 1.3 80.5 - - - +
145A ALA* 1.3 62.1 + - - +
146A ASN* 4.2 13.7 - - - +
246A GLU* 2.8 37.0 + - - -
1272A O4B 5.8 0.8 - - - -
210B ASP* 2.9 24.0 + - - +
211B GLY* 3.7 3.7 - - - +
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Residues in contact with ALA 145 (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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42A ALA* 3.5 26.0 - - + +
43A ASN* 3.7 23.1 - - - -
44A LEU* 3.3 12.4 - - + +
133A LEU* 2.8 37.4 + - + +
144A LYS* 1.3 76.5 - - - +
146A ASN* 1.3 62.1 + - - +
147A GLN* 6.2 0.2 - - - +
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Residues in contact with ASN 146 (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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44A LEU* 4.4 0.7 - - - -
130A THR* 3.8 19.4 - - + +
131A VAL 3.2 8.5 - - - +
132A SER* 3.0 30.5 + - - -
144A LYS* 4.2 12.1 - - - +
145A ALA* 1.3 84.6 + - - +
147A GLN* 1.3 77.8 + - - +
148A GLU* 6.0 0.9 - - + -
1272A O4B 4.8 8.7 - - - +
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Residues in contact with GLN 147 (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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44A LEU* 3.0 38.1 - - + +
45A SER* 4.1 4.4 - - - -
46A LEU* 3.6 34.5 - - + +
130A THR* 3.6 3.4 - - - +
131A VAL* 2.7 39.7 + - + +
146A ASN* 1.3 83.2 + - - +
148A GLU* 1.3 65.7 + - - +
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Residues in contact with GLU 148 (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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46A LEU* 3.6 10.3 - - - +
49A ASN* 3.9 11.1 - - - +
128A LYS* 4.6 17.5 - - + +
129A TYR 3.3 11.9 - - - +
130A THR* 4.6 13.9 + - + +
146A ASN* 6.3 0.4 - - + -
147A GLN* 1.3 84.5 + - - +
149A PHE* 1.3 66.6 - - - +
150A VAL* 6.4 0.4 - - + -
155A LEU* 4.7 5.6 - - + +
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Residues in contact with PHE 149 (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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46A LEU* 4.2 6.5 - - + -
49A ASN* 3.2 25.1 - - - +
51A LEU* 4.0 12.6 - - + -
58A ILE* 3.7 23.8 - - + -
80A ILE* 4.2 8.3 - - + -
118A PHE* 4.2 5.6 - + - -
120A VAL* 3.9 21.5 - - + -
128A LYS* 3.8 1.7 - - - +
129A TYR* 2.8 77.8 + + + +
131A VAL* 3.3 34.8 - - + -
148A GLU* 1.3 76.5 - - - +
150A VAL* 1.3 78.0 + - - +
151A LYS* 5.0 0.7 - - + -
155A LEU* 4.4 1.8 - - - -
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Residues in contact with VAL 150 (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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49A ASN 2.8 17.4 + - - +
50A GLN* 3.8 9.9 - - - +
51A LEU* 2.9 29.3 + - - +
127A GLY 3.4 7.0 - - - +
128A LYS* 4.3 15.5 - - + -
148A GLU* 6.4 0.4 - - + -
149A PHE* 1.3 84.7 - - - +
151A LYS* 1.3 61.5 + - - +
153A VAL* 3.1 35.4 - - + +
154A ASP 4.0 12.8 - - - +
155A LEU* 3.7 29.2 - - + +
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Residues in contact with LYS 151 (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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51A LEU* 3.3 11.4 - - + -
52A ALA 3.7 8.7 - - - +
53A SER 2.9 26.2 + - - -
55A GLY* 3.7 13.7 - - - -
120A VAL* 3.9 20.0 - - + -
121A PRO 3.4 21.3 - - - -
122A GLU 3.1 6.7 + - - -
124A MET* 2.7 23.3 + - + +
125A ALA 3.9 9.9 - - - +
126A ASP* 3.1 21.0 + - - +
127A GLY 2.8 34.9 + - - +
129A TYR* 4.0 18.4 - - + +
149A PHE* 5.0 0.2 - - + -
150A VAL* 1.3 76.7 - - - +
152A GLY* 1.3 62.0 + - - +
153A VAL 3.2 4.4 + - - -
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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