Contacts of the strand formed by residues 55 - 62 (chain 3) in PDB entry 5IY6
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 ASN 55 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 ASN* 3.3 26.3 + - - +
483 HIS* 2.9 57.0 + - + +
493 LEU* 3.1 18.7 - - - +
513 MET* 3.4 22.2 - - - +
523 ASN* 3.5 26.0 + - - +
533 ARG 3.1 9.3 - - - +
543 SER* 1.3 81.0 - - - +
563 LYS* 1.4 60.4 + - - +
1003 LYS* 4.1 8.0 + - - +
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Residues in contact with LYS 56 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 LEU* 3.8 17.8 - - + +
93 ASN* 2.7 52.7 + - - +
103 LEU* 3.2 34.3 - - + +
113 LEU* 3.0 21.5 + - - -
483 HIS* 4.1 8.0 - - - -
493 LEU* 3.9 6.3 - - - -
543 SER 3.4 9.6 - - - +
553 ASN* 1.4 73.5 - - - +
573 LEU* 1.4 63.5 + - - +
1003 LYS* 4.9 14.4 - - - +
1433 TYR* 4.9 7.2 + - - +
1473 MET* 4.0 24.8 - - - +
1513 VAL* 4.7 6.9 - - - +
1573 MET* 4.9 1.1 - - - +
1583 LYS 5.0 0.4 - - - -
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Residues in contact with LEU 57 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 LEU* 4.1 5.0 - - - +
113 LEU* 3.4 13.9 - - + +
133 ILE* 3.9 23.6 - - + -
443 LEU* 6.1 0.2 - - + -
453 GLY* 3.9 28.3 - - - -
483 HIS* 5.3 3.8 - - + +
493 LEU* 4.0 20.3 - - + +
563 LYS* 1.4 78.5 - - - +
583 ALA* 1.3 61.7 - - - +
593 VAL* 4.1 1.8 - - + -
713 TYR* 1.2 102.1 - - + +
723 PRO* 4.9 3.3 - - - +
1003 LYS 5.2 3.1 + - - +
1433 TYR* 5.4 1.7 + - - -
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Residues in contact with ALA 58 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 LEU* 4.1 0.8 - - + +
113 LEU 3.2 5.5 + - - -
123 VAL* 3.8 23.3 - - + +
133 ILE 2.8 25.8 + - - -
573 LEU* 1.3 70.3 - - - +
593 VAL* 1.4 59.9 + - - +
603 ILE* 5.2 6.5 - - + +
693 PHE* 6.4 0.2 - - + -
713 TYR* 1.8 28.3 + - - +
723 PRO* 4.6 8.3 - - + -
1433 TYR* 4.4 22.2 - - + -
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Residues in contact with VAL 59 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ILE* 3.4 16.2 - - + +
153 VAL* 4.4 11.7 - - + -
413 VAL* 6.1 2.5 - - + -
573 LEU* 4.1 1.1 - - + -
583 ALA* 1.4 71.2 - - - +
603 ILE* 1.3 71.9 + - - +
693 PHE* 3.9 1.0 - - - +
703 LEU* 3.0 53.1 + - + -
713 TYR* 2.0 66.2 + - + +
1113 ILE* 4.2 10.5 - - + -
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Residues in contact with ILE 60 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 VAL* 5.4 5.2 - - + -
133 ILE 2.8 9.6 + - - +
143 VAL* 3.3 10.7 - - + -
153 VAL* 2.7 37.3 + - - +
583 ALA* 5.2 6.3 - - + -
593 VAL* 1.3 82.7 - - - +
613 ALA* 1.3 59.3 + - - +
673 SER* 3.2 24.5 - - - +
683 ARG 3.0 15.0 - - - +
693 PHE* 4.0 19.1 - - + -
703 LEU* 4.2 2.5 - - - +
1363 SER* 3.7 26.0 - - - +
1393 LYS* 4.0 9.0 - - + -
1403 ALA* 3.7 26.9 - - + +
1433 TYR* 6.1 0.9 - - + -
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Residues in contact with ALA 61 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153 VAL* 3.3 17.0 - - + +
173 ALA* 4.8 6.5 - - + -
603 ILE* 1.3 77.4 - - - +
623 SER* 1.4 61.5 + - - +
633 HIS* 3.6 0.9 + - - +
663 GLU 4.2 0.2 - - - +
673 SER* 3.3 5.9 + - - -
683 ARG* 2.7 38.8 + - + +
703 LEU* 3.9 22.8 - - + +
1153 ILE* 5.8 1.6 - - + -
1183 LEU* 4.7 18.6 - - + -
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Residues in contact with SER 62 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 VAL* 4.7 5.0 - - - +
153 VAL 2.8 15.0 + - - +
163 ASP* 3.1 5.9 - - - +
173 ALA* 3.0 21.4 + - - -
603 ILE 4.1 0.6 + - - -
613 ALA* 1.4 69.3 - - - +
633 HIS* 1.3 57.6 + - - +
663 GLU 4.4 0.9 - - - -
673 SER* 4.5 0.2 - - - -
1313 THR* 2.6 33.1 + - - -
1323 LEU 3.3 13.7 + - - -
1333 LEU* 3.5 4.3 - - - +
1363 SER* 2.8 34.2 + - - -
1633 VAL* 6.1 0.2 - - - +
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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