Contacts of the helix formed by residues 535 - 543 (chain B) in PDB entry 1EQR
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 LEU 535 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLU* 3.6 7.9 - - - +
141B ARG* 3.2 31.2 - - + +
144B ILE* 4.1 22.4 - - + -
145B THR* 3.5 28.0 - - + -
148B VAL* 5.8 0.4 - - + -
212B ILE* 4.1 5.8 - - + -
230B THR* 2.8 35.4 + - + +
232B ILE* 4.4 21.1 - - + -
533B PHE 3.3 3.6 + - - -
534B GLY* 1.3 69.7 - - - -
536B ASP* 1.3 64.6 + - - +
538B LEU* 3.2 8.1 + - + +
539B THR* 2.9 36.3 + - - +
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Residues in contact with ASP 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 2.4 30.8 + - - +
229B PHE* 3.4 18.1 - - - +
230B THR* 3.4 27.2 + - - +
534B GLY* 3.3 1.5 - - - -
535B LEU* 1.3 75.0 - - - +
537B ARG* 1.3 63.8 + - - +
539B THR* 3.0 5.8 + - - -
540B MET* 2.9 39.0 + - + +
548B ILE* 4.3 12.5 - - + +
551B VAL* 4.1 4.8 - - + +
552B ILE* 3.6 19.9 - - - +
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Residues in contact with ARG 537 (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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224B ASP* 4.0 19.4 + - - +
481B TYR* 3.4 58.3 + - + +
482B GLU 3.9 18.2 - - - +
483B VAL* 4.7 10.1 - - + -
534B GLY* 3.6 11.9 + - - +
536B ASP* 1.3 76.9 - - - +
538B LEU* 1.3 57.8 + - - +
540B MET* 2.8 64.8 + - + +
541B LEU* 2.9 23.6 + - - +
545B THR 5.6 0.2 + - - -
546B ASP* 4.6 10.5 + - - +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ILE* 5.4 1.3 - - + -
232B ILE* 3.8 15.3 - - + -
252B VAL* 5.3 4.7 - - + -
255B LEU* 4.6 17.9 - - + -
256B TRP* 4.2 25.4 - - + -
478B ILE* 4.7 6.3 - - + -
483B VAL* 4.3 20.6 - - + +
533B PHE* 3.4 41.5 - - + -
534B GLY 3.3 10.3 + - - +
535B LEU* 3.2 16.4 + - + +
537B ARG* 1.3 79.3 - - - +
539B THR* 1.3 57.6 + - - +
541B LEU* 3.5 5.1 + - + +
542B LEU* 3.0 40.0 + - + +
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Residues in contact with THR 539 (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 ARG 4.2 2.5 - - - +
141B ARG* 3.6 41.2 + - + +
144B ILE* 4.1 12.5 - - + +
535B LEU* 2.9 22.3 + - - +
536B ASP 3.0 7.8 + - - -
538B LEU* 1.3 74.1 - - - +
540B MET* 1.3 64.4 + - - +
543B THR* 2.9 40.3 + - + +
551B VAL* 3.4 26.7 - - + -
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Residues in contact with MET 540 (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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224B ASP* 4.1 4.7 - - - +
536B ASP* 2.9 11.6 + - + +
537B ARG* 2.8 69.1 + - + +
539B THR* 1.3 75.0 - - - +
541B LEU* 1.3 65.7 + - + +
543B THR* 3.2 2.1 + - - -
544B GLY* 3.1 19.6 + - - -
545B THR* 3.2 23.7 + - - +
546B ASP 4.6 3.1 - - - +
547B ASN 4.3 3.6 - - - +
548B ILE* 3.4 55.6 - - + +
551B VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 541 (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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256B TRP* 4.1 11.2 - - + -
260B LYS* 5.8 0.2 - - - -
425B TRP* 3.4 31.0 - - + -
478B ILE* 3.4 48.9 - - + +
479B ASN* 4.9 4.0 - - - +
481B TYR* 3.8 29.4 - - + -
483B VAL* 3.9 18.4 - - + -
537B ARG* 2.9 18.1 + - - +
538B LEU* 3.6 10.3 - - + +
540B MET* 1.3 79.5 - - + +
542B LEU* 1.3 61.2 + - - +
543B THR 3.2 1.6 + - - -
544B GLY* 3.4 8.0 + - - -
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Residues in contact with LEU 542 (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 THR* 4.5 0.9 - - - +
144B ILE* 3.2 44.9 - - + -
255B LEU* 4.5 14.4 - - + +
256B TRP* 3.5 50.5 - - + -
259B VAL* 4.3 19.3 - - + +
260B LYS* 3.6 40.5 + - + +
538B LEU* 3.0 22.4 + - + +
539B THR 3.5 1.8 + - - +
540B MET 3.3 0.2 - - - -
541B LEU* 1.3 75.3 - - - +
543B THR* 1.3 60.9 + - + +
544B GLY 3.6 0.4 - - - -
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Residues in contact with THR 543 (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 ARG* 3.8 27.3 + - - +
140B THR* 3.4 33.4 - - + +
260B LYS* 5.4 3.4 - - - +
539B THR* 2.9 30.3 + - + +
540B MET 3.7 1.4 + - - -
542B LEU* 1.3 81.0 - - - +
544B GLY* 1.3 66.0 + - - +
545B THR* 3.1 18.7 + - - -
551B VAL* 3.9 4.7 - - - +
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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