Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 1YFL
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ARG* 2.5 33.8 + - - -
94B TYR* 3.5 7.7 - - - -
97B THR* 3.0 22.3 + - - +
98B ARG* 1.3 73.4 - - - +
100B PRO* 1.3 72.0 - - - +
101B LEU* 4.1 5.2 - - - +
102B LEU* 2.8 45.2 + - + +
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Residues in contact with PRO 100 (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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54B PRO 5.8 0.2 - - - +
57B GLU* 3.8 28.0 - - + +
58B MET* 3.8 14.8 - - + +
61B ARG* 3.5 30.3 - - + +
94B TYR* 4.5 2.5 - - + -
98B ARG 3.0 12.9 - - - +
99B ASP* 1.3 88.6 - - - +
101B LEU* 1.3 63.5 + - - +
103B LEU* 2.9 24.0 + - + +
104B TYR 3.1 9.4 + - - -
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Residues in contact with LEU 101 (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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58B MET 6.1 0.2 - - - -
61B ARG* 3.1 33.9 - - + +
62B LEU* 4.6 8.1 - - + -
65B VAL* 3.3 38.6 - - + -
69B ASP* 4.9 6.7 - - + +
70B VAL* 4.7 12.6 - - + -
73B VAL* 3.4 38.4 - - + -
99B ASP* 3.1 6.6 + - - +
100B PRO* 1.3 77.7 - - - +
102B LEU* 1.3 64.6 + - + +
104B TYR* 3.2 20.6 - - + +
105B VAL* 3.3 11.3 + - + +
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Residues in contact with LEU 102 (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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73B VAL* 3.6 25.6 - - + -
77B TYR* 4.4 7.4 - - + +
90B LEU* 3.3 24.6 - - + +
93B ASP* 4.0 23.8 - - + -
94B TYR* 4.0 11.9 - - + +
97B THR* 3.7 24.9 - - + +
99B ASP* 2.8 25.3 + - + +
101B LEU* 1.3 77.9 - - + +
103B LEU* 1.3 66.2 + - - +
105B VAL* 3.1 5.6 + - - +
106B LEU* 3.0 27.1 + - - +
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Residues in contact with LEU 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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54B PRO* 3.7 33.2 - - + +
55B ILE* 4.1 5.6 - - + +
58B MET* 3.9 17.9 - - + -
94B TYR* 3.5 41.3 - - + +
99B ASP 3.6 1.8 + - - -
100B PRO* 2.9 11.3 + - + +
102B LEU* 1.3 77.7 - - - +
104B TYR* 1.3 63.9 + - - +
105B VAL 3.2 0.2 + - - -
106B LEU* 3.2 9.3 + - - +
107B HIS* 3.0 24.3 + - - +
115B ILE* 4.4 11.2 - - + -
117B ILE* 4.7 3.4 - - + -
123B PHE* 3.6 33.7 - - + -
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Residues in contact with TYR 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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4B ALA 4.3 5.9 + - - -
5B ILE* 3.9 18.8 - - + -
58B MET* 3.6 28.3 - - + -
62B LEU* 3.2 43.3 - - + -
67B TRP* 4.6 0.2 - + - -
70B VAL* 4.0 29.4 - - + -
100B PRO 3.1 4.6 + - - +
101B LEU* 3.2 15.5 - - + +
102B LEU 3.1 0.2 - - - -
103B LEU* 1.3 79.7 - - - +
105B VAL* 1.3 58.6 + - + +
107B HIS* 3.0 26.2 + + - -
108B PHE* 3.1 39.4 - + - -
136B SER 4.3 0.3 + - - -
139B ARG* 5.4 0.2 - - - +
140B PHE* 3.4 38.3 + + - +
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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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70B VAL* 4.7 15.0 - - + +
73B VAL* 4.0 28.5 - - + -
74B ILE* 4.3 14.4 - - + -
79B LEU* 3.6 8.1 - - + -
90B LEU* 3.4 23.3 - - + -
101B LEU* 3.3 16.8 + - + +
102B LEU* 3.1 8.1 + - - +
104B TYR* 1.3 75.2 - - + +
106B LEU* 1.3 58.1 + - - +
108B PHE* 2.7 40.2 + - + +
109B HIS* 3.1 23.8 - - - +
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Residues in contact with LEU 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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87B PHE* 4.1 15.9 - - + +
90B LEU* 3.8 16.4 - - + +
91B ARG* 3.6 30.7 - - + +
94B TYR* 3.5 36.8 - - + -
102B LEU 3.0 15.8 + - - +
103B LEU* 3.4 9.2 - - - +
105B VAL* 1.3 76.4 - - - +
107B HIS* 1.3 53.4 + - - +
108B PHE 2.6 0.7 + - - -
109B HIS* 2.5 33.5 + - - +
110B GLY* 3.0 10.4 + - - -
123B PHE* 3.9 40.6 - - + -
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Residues in contact with HIS 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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4B ALA 5.4 0.4 - - - -
5B ILE* 3.4 39.5 - - + +
6B ALA* 3.7 20.7 + - - +
58B MET* 5.3 1.3 - - - -
103B LEU* 3.0 13.9 + - + +
104B TYR* 3.0 21.8 + + - +
105B VAL 3.2 0.2 + - - -
106B LEU* 1.3 77.1 - - - +
108B PHE* 1.3 94.8 + + - +
109B HIS 3.3 0.4 + - - -
110B GLY 4.1 1.8 - - - +
113B ASN* 3.1 33.2 + - + +
114B MET 5.1 2.5 - - - -
115B ILE* 3.9 32.3 - - + -
123B PHE* 4.5 7.0 - - + -
139B ARG* 6.3 0.4 - - - -
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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