Contacts of the helix formed by residues 102 - 112 (chain B) in PDB entry 1YYH
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 ALA 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ALA 3.2 27.4 - - - +
68B SER* 3.4 28.3 - - - +
97B ALA* 2.8 18.6 + - + +
100B ALA* 4.2 4.3 - - + -
101B ASP* 1.3 71.8 - - - +
103B GLN* 1.3 58.4 + - - +
104B GLY 3.3 3.1 + - - -
105B VAL* 3.4 5.1 + - + -
106B PHE* 2.9 28.6 + - - +
139B MET* 3.9 2.0 - - - -
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Residues in contact with GLN 103 (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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101B ASP* 3.2 18.8 + - - +
102B ALA* 1.3 72.0 - - - +
104B GLY* 1.3 57.6 + - - +
106B PHE* 3.4 1.9 + - - +
107B GLN* 2.9 54.8 + - + +
137B GLU* 2.9 31.9 + - - +
138B GLY* 5.6 1.5 - - - -
139B MET* 3.4 27.1 + - - +
142B ASP* 4.8 2.1 - - - +
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Residues in contact with GLY 104 (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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68B SER* 6.2 0.8 - - - -
70B SER* 3.5 18.4 - - - -
102B ALA 3.3 1.2 - - - -
103B GLN* 1.3 80.1 - - - +
105B VAL* 1.3 61.6 + - - +
107B GLN* 3.4 6.0 + - - +
108B ILE* 3.1 25.9 + - - +
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Residues in contact with VAL 105 (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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61B LEU* 5.3 1.6 - - + +
64B ALA 3.7 6.1 - - - +
65B ALA* 3.6 26.5 - - + +
68B SER* 3.9 7.8 - - - +
69B ARG 3.6 43.7 - - - +
70B SER* 3.7 7.0 - - - +
73B ALA* 4.0 16.4 - - + -
97B ALA* 4.4 0.9 - - + -
102B ALA* 3.4 8.9 + - + +
104B GLY* 1.3 71.8 - - - +
106B PHE* 1.3 62.0 + - - +
108B ILE* 3.3 7.2 + - - +
109B LEU* 2.9 45.8 + - + +
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Residues in contact with PHE 106 (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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94B LEU* 3.7 19.1 - - + -
97B ALA* 3.9 10.9 - - + +
98B VAL* 4.2 7.4 - - + -
102B ALA 2.9 19.2 + - - +
103B GLN* 3.4 6.1 - - - +
105B VAL* 1.3 75.9 - - - +
107B GLN* 1.3 87.1 + - - +
109B LEU* 3.2 4.9 + - - +
110B ILE* 2.9 55.5 + - + +
139B MET* 3.5 63.5 - - + -
142B ASP* 3.6 15.3 - - + -
143B LEU* 3.9 15.0 - - + -
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Residues in contact with GLN 107 (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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103B GLN* 2.9 31.3 + - + +
104B GLY* 3.8 5.8 - - - +
105B VAL 3.3 0.2 - - - -
106B PHE* 1.3 91.2 - - - +
108B ILE* 1.3 63.4 + - - +
110B ILE* 3.4 15.5 + - - +
111B ARG* 3.0 52.7 + - - +
142B ASP* 2.8 29.7 + - - +
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Residues in contact with ILE 108 (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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70B SER* 3.4 42.0 - - - +
73B ALA* 4.3 6.1 - - + -
74B LYS* 3.5 35.7 - - + +
77B LEU* 3.6 22.4 - - + -
104B GLY 3.1 16.6 + - - +
105B VAL* 3.6 8.7 - - - +
107B GLN* 1.3 78.3 - - - +
109B LEU* 1.3 62.1 + - - +
111B ARG* 3.5 25.4 + - - +
112B ASN* 3.2 20.4 + - - +
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Residues in contact with LEU 109 (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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61B LEU* 4.3 23.1 - - + -
73B ALA* 5.8 0.2 - - + -
77B LEU* 4.2 20.2 - - + -
83B ALA* 4.8 4.9 - - + +
93B PRO* 3.6 39.7 - - + +
94B LEU* 3.6 17.0 - - + +
97B ALA* 4.2 5.8 - - + -
105B VAL* 2.9 38.2 + - + +
106B PHE 3.7 3.8 - - - +
108B ILE* 1.3 78.2 - - + +
110B ILE* 1.3 61.9 + - - +
112B ASN* 3.3 7.0 + - - -
115B THR* 2.7 41.5 + - + +
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Residues in contact with ILE 110 (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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94B LEU* 3.8 14.6 - - + -
106B PHE* 2.9 63.4 + - + +
107B GLN* 3.6 18.4 - - - +
109B LEU* 1.3 77.5 - - - +
111B ARG* 1.3 63.8 + - + +
112B ASN 3.6 4.3 + - - +
117B LEU* 4.0 20.2 - - + +
142B ASP* 3.9 17.7 - - + +
143B LEU* 3.9 12.8 - - + -
146B SER* 3.8 28.4 + - - +
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Residues in contact with ARG 111 (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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74B LYS* 5.8 3.2 - - - +
107B GLN* 3.0 41.9 + - - +
108B ILE* 3.8 30.0 - - - +
109B LEU 3.2 0.2 - - - -
110B ILE* 1.3 80.0 - - + +
112B ASN* 1.3 61.3 + - - +
113B ARG* 3.5 3.3 + - - -
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Residues in contact with ASN 112 (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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77B LEU* 3.9 29.5 - - + +
83B ALA* 3.7 15.6 - - - +
108B ILE 3.2 12.9 + - - +
109B LEU 3.3 10.6 + - - +
110B ILE 4.1 4.9 - - - +
111B ARG* 1.3 74.3 - - - +
113B ARG* 1.3 66.3 + - - +
114B ALA* 3.8 10.5 + - - +
115B THR* 3.1 45.1 + - - +
117B LEU* 5.8 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