Contacts of the strand formed by residues 151 - 158 (chain B) in PDB entry 1EFU
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 ILE 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A MET* 3.8 29.8 - - + -
61B ILE* 4.4 0.2 - - - -
145B TYR 4.5 0.2 - - - -
146B GLN* 3.4 8.7 + - - -
147B HIS* 2.7 51.5 + - + +
150B ARG* 1.3 86.9 - - + +
152B GLY* 1.3 62.0 + - - +
153B VAL* 4.3 0.9 - - + -
173B ALA* 4.0 19.1 - - + +
257B ARG* 3.4 41.5 - - + +
258B PHE 3.5 11.0 - - - +
259B GLU* 4.0 19.7 - - + +
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Residues in contact with GLY 152 (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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61B ILE* 3.6 12.1 - - - +
72B ILE* 3.1 8.6 - - - +
145B TYR 3.4 2.9 - - - -
146B GLN* 3.4 21.8 - - - -
151B ILE* 1.3 74.1 - - - +
153B VAL* 1.3 65.7 + - - +
258B PHE 2.9 34.0 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 4.1 3.2 - - - +
72B ILE* 4.0 0.6 - - - +
144B SER* 3.1 8.5 - - - -
145B TYR 2.8 37.6 + - - +
151B ILE* 4.3 1.3 - - + -
152B GLY* 1.3 80.8 - - - +
154B LEU* 1.3 67.5 + - - +
155B VAL* 3.9 11.0 - - + -
169B ALA* 3.6 41.3 - - + +
172B VAL* 3.9 12.1 - - + -
173B ALA* 3.7 26.7 - - + +
256B ILE 3.1 11.4 - - - +
257B ARG* 4.0 12.1 - - + -
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Residues in contact with LEU 154 (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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63B THR* 3.7 25.4 - - - -
64B LYS 4.6 0.4 - - - +
65B ILE* 4.1 19.7 - - + -
70B GLY* 3.6 17.9 - - - +
71B ILE 3.6 27.1 - - - +
72B ILE* 3.7 22.4 - - + +
137B LEU* 3.3 24.8 - - + +
142B LEU* 5.9 2.0 - - + -
143B GLY 3.3 2.9 - - - +
144B SER* 3.8 13.5 - - - -
153B VAL* 1.3 73.4 - - - +
155B VAL* 1.3 63.9 + - - +
255B PHE* 3.0 5.0 - - - +
256B ILE* 2.8 35.2 + - + +
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Residues in contact with VAL 155 (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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137B LEU* 3.8 4.5 - - - -
141B VAL 3.6 0.7 - - - +
142B LEU* 3.3 5.8 - - - +
143B GLY 2.8 38.1 + - - +
153B VAL* 3.9 5.8 - - + -
154B LEU* 1.3 79.7 - - - +
156B ALA* 1.3 71.3 + - - +
157B ALA* 4.8 4.0 - - + -
165B VAL* 3.9 24.5 - - + +
168B ILE* 4.1 21.5 - - + -
169B ALA* 3.7 33.9 - - + +
172B VAL* 4.6 1.1 - - + -
252B VAL* 4.5 6.5 - - + -
254B GLY 3.6 6.3 - - - +
255B PHE* 4.0 9.9 - - + -
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Residues in contact with ALA 156 (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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137B LEU* 3.7 7.3 - - + +
138B GLU 3.9 11.2 - - - +
139B GLY* 4.0 4.9 - - - -
141B VAL 3.3 5.4 - - - -
142B LEU* 3.8 17.0 - - + -
155B VAL* 1.3 73.0 - - - +
157B ALA* 1.3 61.3 + - - +
252B VAL* 3.6 5.4 - - - +
253B THR* 2.9 45.5 + - + -
254B GLY* 2.9 17.0 + - - +
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Residues in contact with ALA 157 (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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140B ASP* 3.7 7.3 + - - +
141B VAL* 2.9 35.3 + - + +
155B VAL* 4.2 3.8 - - + -
156B ALA* 1.3 74.6 - - - +
158B LYS* 1.3 61.8 + - - +
160B ALA* 3.8 22.7 - - + -
165B VAL* 4.1 15.7 - - + -
245B LEU* 6.1 0.7 - - + -
251B GLU 3.1 15.5 - - - +
252B VAL* 4.5 7.4 - - + -
253B THR* 4.2 5.8 + - - +
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Residues in contact with LYS 158 (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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140B ASP* 4.2 20.2 + - + +
141B VAL* 5.1 0.4 - - - -
157B ALA* 1.3 75.3 - - - +
159B GLY* 1.3 64.6 + - - +
160B ALA 3.3 0.4 - - - -
249B ASN 5.4 3.1 - - - +
250B ALA* 3.2 5.2 - - - -
251B GLU* 2.8 59.2 + - + +
253B THR* 4.8 9.0 - - - +
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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