Contacts of the helix formed by residues 1013 - 1021 (chain B) in PDB entry 1Y1V
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 ASN1013 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A GLN* 4.2 2.4 + - - -
526A ASP* 2.7 24.7 + - - -
827B ILE* 4.3 1.3 - - - +
829B CYS* 3.6 3.5 - - - -
834B ASN* 3.4 28.0 + - - +
835B GLN* 3.0 30.0 - - - +
836B GLU 3.9 4.8 - - - +
837B ASP 5.3 2.5 - - - +
1012B ILE* 1.3 72.4 - - - +
1014B PRO* 1.3 77.3 - - - +
1015B HIS* 3.0 27.0 + - + +
1016B ALA* 2.8 39.1 + - + +
1017B ILE* 5.5 0.5 - - - +
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Residues in contact with PRO1014 (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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662A PHE* 3.9 19.5 - - + +
663A SER 4.0 4.9 - - - +
664A THR* 3.1 31.2 - - + +
746A MET* 3.9 5.7 - - - +
827B ILE* 3.5 17.0 - - + -
828B ALA 4.0 10.5 - - - -
829B CYS* 3.8 20.4 - - - -
1012B ILE 3.7 6.7 - - - +
1013B ASN* 1.3 94.3 - - - +
1015B HIS* 1.3 55.0 + - + +
1016B ALA 2.8 6.7 + - - -
1017B ILE* 2.9 18.2 + - + +
1018B PRO* 3.2 12.6 - - - +
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Residues in contact with HIS1015 (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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525A GLN* 3.1 51.2 - - + +
526A ASP* 3.5 4.5 + - - -
529A CYS* 3.3 26.0 - - + +
662A PHE* 4.3 2.8 - + - -
746A MET* 3.0 27.6 - - + -
751A SER* 2.7 29.6 + - - -
752A LYS* 3.7 39.3 + - + +
829B CYS* 4.8 1.9 - - - -
1013B ASN* 2.9 19.3 + - - +
1014B PRO* 1.3 75.2 - - - +
1016B ALA* 1.3 54.6 + - - +
1017B ILE 3.1 4.0 + - - -
1018B PRO* 4.5 2.1 - - - +
1019B SER* 4.3 4.5 + - - -
1020B ARG* 4.9 2.4 + - - -
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Residues in contact with ALA1016 (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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837B ASP* 4.4 17.7 - - - +
986B GLN* 3.1 33.9 + - + -
1012B ILE* 5.9 2.9 - - + -
1013B ASN* 2.8 20.2 + - + +
1015B HIS* 1.3 78.5 - - - +
1017B ILE* 1.3 61.2 + - + +
1020B ARG* 3.4 29.7 - - - +
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Residues in contact with ILE1017 (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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664A THR* 3.7 24.7 - - + -
743A VAL* 5.8 1.3 - - + -
761A MET* 5.3 10.3 - - + -
827B ILE* 5.4 8.5 - - + -
986B GLN* 4.1 2.7 - - - +
1012B ILE* 6.5 0.9 - - + -
1013B ASN 5.5 0.2 - - - +
1014B PRO* 2.9 14.2 + - + +
1015B HIS 3.1 2.4 + - - -
1016B ALA* 1.3 83.6 - - + +
1018B PRO* 1.3 86.7 - - + +
1019B SER 3.7 0.4 - - - -
1020B ARG 3.0 3.7 + - - -
1021B MET* 2.6 20.1 + - - -
1022B THR* 3.3 43.0 + - + +
1025B HIS* 5.1 9.4 - - + +
1026B LEU* 4.4 20.9 - - + -
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Residues in contact with PRO1018 (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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743A VAL* 4.1 21.8 - - + -
746A MET* 3.4 28.9 - - + -
752A LYS* 4.4 7.9 - - + +
753A GLY* 4.2 19.3 - - - +
757A ASN* 4.3 7.4 - - + -
761A MET* 4.8 7.4 - - + -
1014B PRO 3.2 17.3 - - - +
1015B HIS* 4.5 4.5 - - - +
1017B ILE* 1.3 98.4 - - + +
1019B SER* 1.3 56.3 + - - +
1020B ARG 2.6 1.4 + - - -
1021B MET* 2.5 32.9 + - + +
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Residues in contact with SER1019 (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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752A LYS* 3.5 36.6 + - - +
753A GLY* 4.5 4.9 - - - -
757A ASN* 3.9 26.3 - - - +
763B GLN* 4.5 7.6 + - - -
1015B HIS 4.3 4.0 + - - -
1018B PRO* 1.3 77.2 - - - +
1020B ARG* 1.3 66.6 + - - +
1021B MET* 3.4 0.7 - - - +
291S GLU 4.3 6.9 - - - +
292S PRO* 3.7 20.2 - - - +
293S LEU* 5.0 1.4 - - - +
309S SER 5.2 8.7 - - - -
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Residues in contact with ARG1020 (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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752A LYS* 4.3 17.9 - - - +
763B GLN* 4.3 6.3 - - - +
766B ARG* 2.7 54.4 + - - +
836B GLU* 5.9 0.6 - - - +
837B ASP* 3.0 34.5 + - - +
985B GLY 5.3 0.2 - - - -
986B GLN* 3.3 23.5 + - - +
1015B HIS 4.9 1.0 + - - -
1016B ALA* 3.4 31.0 - - - +
1017B ILE 3.0 5.4 + - - +
1018B PRO 2.6 6.1 + - - -
1019B SER* 1.3 83.2 + - - +
1021B MET* 1.3 68.2 + - - +
1022B THR* 3.1 7.5 + - + -
290S ASP 2.7 28.7 + - - -
291S GLU* 3.4 17.8 + - - +
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Residues in contact with MET1021 (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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757A ASN* 3.5 43.7 - - - +
760A GLN* 3.9 27.1 - - - +
761A MET* 3.4 29.8 - - + -
804A TYR* 3.9 20.1 - - + +
762B ASN* 4.1 2.4 - - - -
763B GLN* 3.5 44.0 + - + +
1017B ILE* 2.6 8.0 + - - -
1018B PRO 2.5 29.5 + - - +
1019B SER 4.7 0.9 - - - +
1020B ARG* 1.3 70.2 - - - +
1022B THR* 1.3 57.8 + - - +
1023B VAL* 3.4 10.1 + - - +
293S LEU* 5.2 1.6 - - + -
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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