Contacts of the helix formed by residues 115 - 124 (chain I) in PDB entry 1YHQ
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 ASP 115 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113I SER* 3.8 4.3 + - - -
114I TYR* 1.3 88.1 - - - +
116I LEU* 1.3 66.2 + - - +
117I THR* 3.2 15.6 + - - +
118I ASN* 3.4 21.2 + - - +
119I ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ALA* 4.8 7.8 - - + +
105I GLU* 6.0 4.3 - - + -
108I HIS* 3.5 33.2 - - + +
114I TYR 5.9 0.7 - - - +
115I ASP* 1.3 74.2 - - - +
117I THR* 1.3 62.4 + - - +
119I ALA* 3.4 9.2 + - + +
120I ALA* 3.2 21.8 + - - +
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Residues in contact with THR 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I ASP* 3.0 12.4 - - - +
116I LEU* 1.3 80.1 - - - +
118I ASN* 1.3 64.7 + - - +
120I ALA* 3.4 16.0 + - - +
121I LYS* 3.4 25.4 - - - +
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Residues in contact with ASN 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11850 U 3.8 14.5 - - - +
11860 C 3.4 22.8 + - - -
113I SER* 3.4 18.6 - - - -
114I TYR* 4.5 0.4 - - - +
115I ASP* 3.4 33.1 + - - +
117I THR* 1.3 72.7 - - - +
119I ALA* 1.3 67.7 + - - +
120I ALA 3.0 2.5 - - - -
121I LYS* 2.8 57.1 + - - +
122I GLU* 3.3 8.9 + - - +
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Residues in contact with ALA 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ALA* 4.4 17.3 - - + +
108I HIS* 5.5 3.4 - - - +
111I LEU* 3.4 22.9 - - + +
113I SER* 3.2 20.3 + - - +
115I ASP 3.2 8.3 + - - +
116I LEU* 3.5 16.2 - - + +
118I ASN* 1.3 78.3 - - - +
120I ALA* 1.3 61.4 + - - +
122I GLU* 3.5 3.1 + - - +
123I VAL* 3.3 24.3 + - - +
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I VAL* 4.7 9.9 - - + +
101I LYS* 6.1 2.2 - - + -
104I ALA* 4.4 13.0 - - + +
116I LEU 3.2 8.7 + - - +
117I THR* 3.4 11.4 - - - +
118I ASN 3.0 0.4 - - - -
119I ALA* 1.3 77.5 - - - +
121I LYS* 1.3 54.3 + - - +
123I VAL* 2.8 10.0 + - - -
124I VAL* 2.7 47.9 + - + +
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Residues in contact with LYS 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11840 C 3.6 34.3 - - - +
11850 U 2.9 27.7 + - - +
117I THR* 3.4 26.2 - - - +
118I ASN* 2.8 44.1 + - - +
120I ALA* 1.3 72.1 - - - +
122I GLU* 1.3 60.6 + - - +
124I VAL* 3.5 9.9 + - - +
125I GLY 3.4 13.3 + - - -
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Residues in contact with GLU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11620 G 3.3 16.1 + - - +
11630 G 3.9 22.7 + - - +
11840 C 4.0 15.0 - - - +
11850 U 3.4 29.7 + - - +
111I LEU* 3.1 40.6 - - + +
112I LEU 4.3 2.1 + - - -
113I SER* 3.0 33.1 + - - -
118I ASN 3.7 5.6 - - - +
119I ALA* 3.7 7.8 - - - +
120I ALA 3.1 0.4 - - - -
121I LYS* 1.3 76.6 - - - +
123I VAL* 1.3 62.9 + - - +
125I GLY* 3.2 12.6 + - - -
126I THR* 3.9 9.2 + - - -
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Residues in contact with VAL 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11630 G 5.2 5.8 - - - +
70I THR* 4.3 17.0 - - + +
74I ILE* 5.3 0.4 - - + -
100I VAL* 4.3 15.0 - - + -
103I ILE* 3.7 46.4 - - + +
104I ALA* 4.7 5.2 - - + -
107I LYS* 5.3 5.6 - - + -
111I LEU* 4.4 11.0 - - + -
119I ALA 3.3 18.4 - - - +
120I ALA* 2.8 12.2 + - - +
122I GLU* 1.3 68.0 - - + +
124I VAL* 1.3 52.5 + - - +
125I GLY 2.8 14.9 + - - -
126I THR* 3.2 14.6 + - - -
127I CYS* 3.4 16.0 - - - -
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Residues in contact with VAL 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11830 C 4.8 2.3 + - - -
11840 C 5.9 0.9 - - - +
100I VAL* 3.4 26.5 - - + -
120I ALA* 2.7 31.4 + - + +
121I LYS* 3.7 11.2 - - - +
122I GLU 3.4 0.2 - - - -
123I VAL* 1.3 68.9 - - - +
125I GLY* 1.3 56.6 + - - +
126I THR 3.6 0.9 - - - -
127I CYS* 4.4 11.7 + - + +
128I THR* 4.3 16.5 + - - +
134I ILE* 3.4 31.0 - - + -
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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