Contacts of the helix formed by residues 99 - 110 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E ARG* 2.6 32.0 + - - -
94E TYR* 3.2 14.4 - - - -
97E THR* 3.1 19.0 + - - +
98E ARG* 1.3 75.3 - - - +
100E PRO* 1.3 69.0 - - - +
101E LEU* 3.0 12.6 + - - +
102E LEU* 3.1 33.0 + - + +
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Residues in contact with PRO 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PRO 5.2 0.9 - - - +
57E GLU* 3.5 40.8 - - + +
58E MET* 3.6 14.3 - - + +
61E ARG* 3.6 18.6 - - + +
94E TYR* 4.5 1.8 - - + +
98E ARG 3.1 10.1 - - - +
99E ASP* 1.3 86.2 - - - +
101E LEU* 1.3 53.4 + - - +
103E LEU* 2.6 36.1 + - + +
104E TYR* 2.9 10.2 + - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E MET* 5.8 0.2 - - - -
61E ARG* 3.3 38.9 - - + +
62E LEU* 5.2 1.8 - - + -
65E VAL* 4.7 15.9 - - + -
69E ASP* 4.5 10.8 - - + +
70E VAL* 4.4 18.8 - - + -
73E VAL* 3.3 34.1 - - + -
99E ASP* 3.0 12.9 + - - +
100E PRO* 1.3 73.0 - - - +
102E LEU* 1.3 67.3 + - + +
104E TYR* 3.5 12.8 + - + +
105E VAL* 3.0 26.3 + - + +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E VAL* 3.5 31.9 - - + -
77E TYR* 4.2 18.2 - - + +
90E LEU* 3.5 19.8 - - + +
93E ASP* 4.4 3.4 - - + -
94E TYR* 4.1 28.7 - - + +
97E THR* 4.3 11.4 - - + +
99E ASP* 3.1 25.0 + - + +
100E PRO 2.8 3.0 + - - -
101E LEU* 1.3 78.6 - - + +
103E LEU* 1.3 60.5 + - - +
104E TYR 3.2 0.2 - - - -
105E VAL* 3.1 5.2 + - - +
106E LEU* 2.9 32.2 + - - +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E PRO* 3.4 34.8 - - + +
55E ILE* 4.5 2.9 - - - +
58E MET* 3.9 17.5 - - + -
94E TYR* 3.4 39.4 - - + +
99E ASP 3.5 1.8 + - - -
100E PRO* 2.6 15.8 + - + +
102E LEU* 1.3 72.0 - - - +
104E TYR* 1.3 66.8 + - - +
106E LEU* 3.0 16.9 + - + +
107E HIS* 3.1 13.2 + - - +
115E ILE* 4.4 14.6 - - + -
117E ILE* 5.3 2.0 - - + -
123E PHE* 3.6 35.0 - - + -
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Residues in contact with TYR 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ALA 4.6 4.4 + - - -
5E ILE* 3.9 12.3 - - + -
58E MET* 3.3 33.8 - - + -
62E LEU* 3.5 41.5 - - + -
67E TRP* 4.0 1.3 - + - -
70E VAL* 3.8 28.7 - - + -
100E PRO 2.9 7.8 + - - +
101E LEU* 3.5 16.6 - - + +
103E LEU* 1.3 77.2 - - - +
105E VAL* 1.3 61.8 + - - +
107E HIS* 2.6 45.0 + + - -
108E PHE* 3.4 32.8 - + - -
136E SER 4.5 0.5 + - - -
139E ARG* 5.5 0.5 - - - +
140E PHE* 3.8 29.0 + + - +
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E VAL* 4.5 13.9 - - + -
73E VAL* 3.7 32.3 - - + -
74E ILE* 3.9 19.1 - - + -
79E LEU* 4.1 2.2 - - + -
90E LEU* 3.9 13.9 - - + -
101E LEU* 3.0 25.1 - - + +
102E LEU 3.1 7.8 + - - +
104E TYR* 1.3 77.9 - - + +
106E LEU* 1.3 59.8 + - - +
108E PHE* 3.3 16.0 + - + +
109E HIS* 2.9 41.7 + - + -
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E PHE* 4.1 21.9 - - + +
90E LEU* 3.5 28.9 - - + -
91E ARG* 3.6 21.5 - - + +
94E TYR* 3.8 33.0 - - + -
102E LEU 2.9 15.1 + - - +
103E LEU* 3.0 10.1 + - - +
105E VAL* 1.3 74.6 - - - +
107E HIS* 1.3 54.9 + - - +
108E PHE 2.7 0.5 + - - -
109E HIS* 2.6 34.4 + - - +
110E GLY 3.3 7.5 + - - -
123E PHE* 3.7 36.8 - - + -
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Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.4 35.2 - - + +
6E ALA* 4.3 11.0 + - - +
58E MET* 5.4 1.6 - - + -
103E LEU 3.1 7.5 + - - +
104E TYR* 2.6 37.3 + + - +
105E VAL 3.4 0.2 - - - -
106E LEU* 1.3 78.3 - - - +
108E PHE* 1.3 105.0 + + - +
109E HIS 3.2 0.4 + - - -
110E GLY 3.8 2.2 + - - +
113E ASN* 2.9 40.2 + - + +
114E MET 5.0 2.5 - - - -
115E ILE* 3.9 27.8 - - + -
123E PHE* 4.5 10.4 - - + -
139E ARG* 6.0 0.2 - - - -
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Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 5.9 0.2 - - + -
67E TRP* 4.2 6.5 - + - -
70E VAL* 4.6 3.4 - - + -
104E TYR* 3.4 50.3 - + - -
105E VAL* 3.3 14.1 + - + +
106E LEU 2.7 3.8 + - - -
107E HIS* 1.3 107.6 + + - +
109E HIS* 1.3 62.8 + - - +
110E GLY 3.6 0.2 - - - -
113E ASN* 3.5 10.8 + - - +
130E ARG* 3.2 24.8 - - - +
131E THR* 4.1 3.6 - - - -
132E ILE* 3.5 31.4 - - + +
133E ASN* 5.8 0.2 - - - -
136E SER* 3.1 42.2 - - - -
139E ARG* 5.6 6.3 - - + -
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Residues in contact with HIS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E ILE* 4.6 9.1 - - + +
79E LEU* 3.5 41.6 - - + +
80E SER 4.6 5.2 - - - -
83E SER* 5.2 0.2 - - - -
87E PHE* 3.6 19.0 - + + -
90E LEU* 4.7 1.8 - - - +
105E VAL* 2.9 37.0 + - + -
106E LEU* 2.6 15.9 + - - +
108E PHE* 1.3 77.0 - - + +
110E GLY* 1.3 57.4 + - - +
127E PHE* 3.5 14.9 - + + -
128E GLY* 2.7 23.9 + - - -
130E ARG* 3.2 21.8 - - - +
131E THR* 2.5 34.6 + - - -
132E ILE 4.5 1.6 + - - -
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Residues in contact with GLY 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E PHE* 4.2 5.4 - - - -
106E LEU 3.3 7.1 + - - -
107E HIS 3.8 4.5 + - - -
108E PHE 3.6 2.4 - - - -
109E HIS* 1.3 75.6 - - - +
111E PHE* 1.3 55.4 + - - -
112E SER 2.7 18.0 + - - -
113E ASN* 2.8 13.9 + - - -
114E MET 5.1 1.1 - - - -
123E PHE* 5.3 2.0 - - - -
125E THR* 3.8 11.4 - - - -
126E PRO 3.4 9.9 - - - -
128E GLY* 3.3 6.5 - - - -
130E ARG* 3.3 12.1 + - - -
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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