Contacts of the strand formed by residues 142 - 151 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASP* 3.7 40.6 - - + +
212A LEU* 3.6 31.6 - - + -
243A PRO* 4.2 15.0 - - + -
135B VAL 3.5 6.7 - - - +
136B VAL* 4.5 6.5 - - + -
140B GLY 3.7 12.8 - - - +
141B LYS* 1.3 74.3 - - - +
143B PHE* 1.3 68.2 + - - +
144B LYS* 4.1 13.4 - - + +
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Residues in contact with PHE 143 (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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39B VAL* 3.8 16.6 - - + -
40B ILE* 3.2 65.3 - - + +
42B ALA* 4.7 8.5 - - + +
135B VAL* 2.8 47.7 + - + +
137B ALA* 4.1 6.5 - - + -
141B LYS* 3.5 41.5 - - + -
142B VAL* 1.3 77.2 - - - +
144B LYS* 1.3 67.1 + - - +
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Residues in contact with LYS 144 (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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210A ASP 2.8 24.0 + - - +
211A GLY* 3.7 3.7 + - - +
42B ALA* 4.4 10.4 - - - +
132B SER* 4.3 2.9 - - - +
133B LEU 3.2 12.3 - - - +
134B GLN* 4.0 26.2 - - + +
142B VAL* 4.1 12.5 + - + -
143B PHE* 1.3 81.5 - - - +
145B ALA* 1.3 62.2 + - - +
146B ASN* 4.2 14.8 - - - +
246B GLU* 2.7 37.2 + - - -
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Residues in contact with ALA 145 (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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42B ALA* 3.5 25.8 - - + +
43B ASN* 3.7 24.0 - - - -
44B LEU* 3.3 12.6 - - + +
133B LEU* 2.8 36.7 + - + +
144B LYS* 1.3 75.3 - - - +
146B ASN* 1.3 63.0 + - - +
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Residues in contact with ASN 146 (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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44B LEU* 5.2 0.2 - - - -
130B THR* 3.8 19.3 - - + +
131B VAL 3.2 8.5 - - - +
132B SER* 3.1 28.4 + - - -
144B LYS* 4.2 13.5 - - - +
145B ALA* 1.3 85.2 + - - +
147B GLN* 1.3 78.0 + - - +
148B GLU* 6.0 0.7 - - + -
1272B O4B 5.5 6.1 - - - +
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Residues in contact with GLN 147 (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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44B LEU* 3.0 38.9 - - + +
45B SER* 4.1 5.4 - - - -
46B LEU* 3.6 33.1 - - + +
49B ASN* 5.4 4.8 - - - +
130B THR* 3.6 3.1 - - - +
131B VAL* 2.7 40.1 + - + +
146B ASN* 1.3 83.0 + - - +
148B GLU* 1.3 65.5 + - - +
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Residues in contact with GLU 148 (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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46B LEU* 3.6 4.9 - - - +
49B ASN* 3.6 20.3 + - - +
128B LYS* 4.0 26.6 - - + +
129B TYR 3.3 11.7 - - - +
130B THR* 4.6 13.2 + - + +
146B ASN* 6.0 0.4 - - + -
147B GLN* 1.3 82.3 + - - +
149B PHE* 1.3 67.4 + - - +
150B VAL* 6.4 0.2 - - + -
155B LEU* 4.9 11.0 - - + +
156B ASN* 4.4 15.2 + - - -
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Residues in contact with PHE 149 (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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46B LEU* 4.2 6.3 - - + -
49B ASN* 3.2 25.4 - - - +
51B LEU* 4.0 12.8 - - + -
58B ILE* 3.8 23.3 - - + -
80B ILE* 4.2 8.1 - - + -
118B PHE* 4.2 5.8 - + - -
120B VAL* 3.9 21.8 - - + -
128B LYS* 3.9 1.4 - - - +
129B TYR* 2.8 76.9 + + + +
131B VAL* 3.3 34.8 - - + -
148B GLU* 1.3 76.7 - - - +
150B VAL* 1.3 78.2 + - - +
151B LYS* 5.0 0.4 - - + -
155B LEU* 5.5 2.5 - - - -
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Residues in contact with VAL 150 (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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49B ASN 2.8 16.9 + - - +
50B GLN* 4.0 9.9 - - + +
51B LEU* 2.9 29.8 + - - +
127B GLY 3.4 7.4 - - - +
128B LYS* 4.3 14.6 - - + -
149B PHE* 1.3 85.6 - - - +
151B LYS* 1.3 59.8 + - - +
153B VAL* 3.1 35.9 - - + +
154B ASP 4.0 12.3 - - - +
155B LEU* 3.6 31.0 - - + +
156B ASN 4.7 1.8 - - - +
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Residues in contact with LYS 151 (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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51B LEU* 3.3 11.0 - - + -
52B ALA 3.7 9.0 - - - +
53B SER 2.9 27.1 + - - -
55B GLY* 3.7 13.2 - - - -
120B VAL* 3.9 19.7 - - + -
121B PRO 3.4 21.5 - - - -
122B GLU 3.1 6.3 + - - -
124B MET 2.7 23.5 + - - +
125B ALA 3.9 9.9 - - - +
126B ASP* 3.1 21.0 + - - +
127B GLY 2.8 35.0 + - - +
129B TYR* 4.0 18.6 - - + +
149B PHE* 5.0 0.4 - - + -
150B VAL* 1.3 76.1 - - - +
152B GLY* 1.3 61.2 + - - +
153B VAL 3.3 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