Contacts of the helix formed by residues 602 - 608 (chain O) in PDB entry 5I2D
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 SER 602 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540O LEU* 4.1 10.1 - - - -
543O LEU* 4.2 2.7 - - - -
580O ALA 3.6 6.1 - - - -
581O LEU 3.5 14.8 - - - -
582O LEU 3.8 2.5 + - - -
583O ASP* 3.8 4.3 + - - -
584O ASN* 3.0 35.4 + - - -
600O LEU 3.5 1.6 + - - -
601O ARG* 1.3 74.0 - - - +
603O LEU* 1.3 65.8 + - - +
605O ASP* 3.0 23.9 + - - -
606O ILE* 3.1 25.3 + - - +
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Residues in contact with LEU 603 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091N GLU* 4.3 20.3 - - + +
1094N ALA* 3.7 42.8 - - + +
1095N LEU* 3.8 29.8 - - + -
520O LEU* 4.7 2.7 - - + -
540O LEU* 3.8 29.3 - - + +
544O TYR* 4.8 7.4 - - - +
581O LEU* 3.8 18.3 + - + +
582O LEU* 3.7 9.3 + - + +
602O SER* 1.3 74.8 - - - +
604O THR* 1.3 57.6 + - - +
606O ILE* 3.1 10.5 + - + +
607O LEU* 2.9 31.6 + - + +
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Residues in contact with THR 604 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095N LEU* 4.4 0.6 - - - +
103O TRP* 3.0 30.9 + - + -
582O LEU 3.0 15.4 + - - -
583O ASP* 3.4 34.0 - - - +
602O SER* 3.3 0.4 - - - -
603O LEU* 1.3 77.6 - - - +
605O ASP* 1.3 57.4 + - - +
607O LEU* 3.2 5.4 + - - +
608O SER* 2.7 44.7 + - - +
1444O THR* 3.6 22.0 - - + -
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Residues in contact with ASP 605 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583O ASP* 4.7 4.2 - - - +
584O ASN 4.0 13.0 - - - +
600O LEU 4.0 8.3 - - - +
601O ARG* 3.4 31.2 + - + +
602O SER* 3.0 31.4 + - - +
603O LEU 3.3 0.4 - - - -
604O THR* 1.3 79.7 - - - +
606O ILE* 1.3 58.3 + - - +
608O SER* 2.9 23.2 - - - +
612O GLY 4.7 0.2 + - - -
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Residues in contact with ILE 606 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091N GLU* 3.4 33.2 - - - +
524O LEU 6.1 0.4 - - - +
538O SER* 5.4 2.5 - - - +
540O LEU* 3.8 31.6 - - + -
601O ARG* 3.6 35.6 + - + +
602O SER 3.1 17.6 + - - +
603O LEU* 3.4 10.8 - - + +
605O ASP* 1.3 78.1 - - - +
607O LEU* 1.3 51.5 + - + +
612O GLY* 3.2 4.5 - - - -
613O ARG* 2.6 48.1 + - - +
318Q GLU* 5.7 2.9 - - - +
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Residues in contact with LEU 607 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088N LEU* 3.8 26.2 - - + -
1091N GLU* 4.1 27.6 - - + +
1092N LEU* 3.6 27.8 - - + -
1095N LEU* 3.6 26.7 - - + -
103O TRP* 4.6 2.9 - - + -
603O LEU 2.9 17.0 + - - +
604O THR* 3.2 5.6 + - - +
606O ILE* 1.3 77.7 - - - +
608O SER* 1.3 60.2 + - - +
609O GLY 5.2 0.2 - - - +
612O GLY* 3.8 0.3 - - - -
613O ARG* 3.3 19.8 + - + +
614O PHE* 3.6 26.0 + - + +
1443O THR* 5.0 6.7 - - + -
1447O LEU* 4.4 11.0 - - + -
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Residues in contact with SER 608 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604O THR* 2.7 33.0 + - - +
605O ASP* 2.9 20.8 - - - +
607O LEU* 1.3 78.1 - - - +
609O GLY* 1.3 63.7 + - - +
612O GLY* 3.5 6.0 + - - -
614O PHE* 5.5 0.4 - - - -
1443O THR* 3.5 32.8 - - - -
1444O THR* 5.1 2.8 - - - +
-3U G 5.9 2.7 - - - -
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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