Contacts of the helix formed by residues 108 - 117 (chain A) in PDB entry 1YH8
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 GLY 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A HIS* 5.3 0.2 - - - -
83A VAL* 3.6 9.3 - - - +
107A SER* 1.3 76.4 - - - +
109A TRP* 1.3 58.1 + - - +
110A GLU 3.6 1.8 - - - -
111A PHE* 3.5 10.0 + - - -
112A TYR* 2.8 33.7 + - - +
187A VAL* 2.9 11.7 + - - -
241A PHE* 3.6 27.4 - - - -
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Residues in contact with TRP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP* 4.7 7.6 + - - +
107A SER* 3.3 15.8 + - - +
108A GLY* 1.3 76.7 - - - +
110A GLU* 1.3 70.0 + - + +
112A TYR* 3.1 7.9 + + - +
113A GLU* 2.8 68.5 + - + +
116A ARG* 5.1 0.2 - - - -
184A GLU* 4.4 17.5 - - + -
187A VAL* 2.9 21.2 + - + +
188A LEU* 3.4 39.0 - - + -
230A ARG* 5.4 0.2 - - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.6 25.0 - - + +
14A GLU 5.4 1.0 + - - +
104A LEU* 3.5 39.1 - - + +
105A ASP* 5.2 4.0 + - - +
107A SER 5.4 0.4 + - - -
108A GLY 3.6 0.2 - - - -
109A TRP* 1.3 85.8 - - + +
111A PHE* 1.3 64.5 + - - +
113A GLU* 3.5 4.3 + - - +
114A ALA* 3.2 22.6 + - + +
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.5 45.5 - + + -
26A LEU* 3.9 18.8 - - + -
79A HIS* 4.4 5.6 - - + -
80A ILE* 3.6 45.5 - - + -
83A VAL* 3.9 13.9 - - + -
101A ILE* 4.0 4.3 - - + -
102A PRO* 3.8 23.6 - - + -
104A LEU* 3.7 16.1 - - + +
107A SER 4.9 1.8 - - - -
108A GLY* 3.5 14.9 + - - +
109A TRP 3.3 0.4 - - - -
110A GLU* 1.3 78.5 - - - +
112A TYR* 1.3 62.4 + - - +
114A ALA* 4.0 0.3 - - - +
115A ILE* 3.0 30.7 + - + +
601A CL 4.4 11.2 - - + -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A VAL* 3.6 14.8 - - + +
86A LEU* 4.9 3.8 - - + -
87A LEU* 3.3 36.2 - - + +
108A GLY 2.8 23.6 + - - +
109A TRP* 3.5 5.8 - + - +
111A PHE* 1.3 74.6 - - - +
113A GLU* 1.3 68.7 + - - +
116A ARG* 2.9 71.4 + - - +
183A GLU* 3.5 35.9 + - + +
184A GLU* 3.9 18.2 + - + +
187A VAL* 3.8 28.9 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TRP* 2.8 74.3 + - + +
110A GLU* 4.0 4.7 - - - +
112A TYR* 1.3 77.3 - - - +
114A ALA* 1.3 61.8 + - - +
116A ARG* 2.6 46.5 + - - +
117A LYS* 3.0 46.3 + - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.0 11.7 - - + -
13A PHE* 3.6 30.7 - - + -
110A GLU* 3.2 9.2 + - + +
113A GLU* 1.3 79.6 - - - +
115A ILE* 1.3 65.8 + - - +
116A ARG 3.4 0.3 + - - -
117A LYS* 3.5 10.1 + - - +
118A ASN* 3.0 26.4 + - - +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.7 10.5 - - + -
11A LEU* 3.7 21.8 - - + -
13A PHE* 4.6 9.4 - - + -
28A ILE* 5.2 7.0 - - + -
80A ILE* 4.1 20.9 - - + -
83A VAL* 4.1 8.7 - - + -
84A LEU* 3.8 22.9 - - + -
87A LEU* 3.4 18.8 - - + -
89A ILE* 3.7 26.2 - - + -
111A PHE* 3.0 20.2 + - + +
114A ALA* 1.3 74.4 - - - +
116A ARG* 1.3 63.5 + - - +
118A ASN 3.1 12.8 + - - -
120A ILE* 3.3 11.8 + - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.6 21.2 - - + +
109A TRP* 5.0 0.4 - - - -
112A TYR* 2.9 42.2 + - - +
113A GLU* 2.6 49.1 + - - +
114A ALA 3.2 0.2 - - - -
115A ILE* 1.3 78.5 - - - +
117A LYS* 1.3 64.7 + - - +
118A ASN 3.3 0.2 - - - -
120A ILE* 3.6 21.4 + - + +
184A GLU* 3.4 27.1 + - - -
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 3.5 16.2 + - - -
113A GLU* 3.0 43.6 + - - +
114A ALA* 3.7 9.9 - - - +
115A ILE 3.3 0.2 - - - -
116A ARG* 1.3 84.8 - - + +
118A ASN* 1.3 68.9 + - - +
120A ILE 3.7 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