Contacts of the helix formed by residues 99 - 110 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D ARG* 2.6 31.8 + - - -
94D TYR* 3.2 14.2 - - - -
97D THR* 3.1 19.3 + - - +
98D ARG* 1.3 76.2 - - - +
100D PRO* 1.3 70.3 - - - +
101D LEU* 3.0 13.0 + - - +
102D LEU* 3.1 33.0 + - + +
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Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO 5.2 0.9 - - - +
57D GLU* 3.5 42.0 - - + +
58D MET* 3.6 13.1 - - + +
61D ARG* 3.6 18.8 - - + +
94D TYR* 4.5 1.3 - - + +
98D ARG 3.1 11.4 - - - +
99D ASP* 1.3 86.0 - - - +
101D LEU* 1.3 54.5 + - - +
103D LEU* 2.6 35.5 + - + +
104D TYR* 2.9 10.4 + - - +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET* 5.7 0.2 - - - -
61D ARG* 3.3 40.0 - - + +
62D LEU* 5.2 2.5 - - + -
65D VAL* 4.6 16.4 - - + -
69D ASP* 4.6 9.9 - - + +
70D VAL* 4.5 19.7 - - + +
73D VAL* 3.3 34.5 - - + -
99D ASP* 3.0 12.9 + - - +
100D PRO* 1.3 73.6 - - - +
102D LEU* 1.3 68.2 + - + +
104D TYR* 3.4 12.3 + - + +
105D VAL* 3.1 27.5 + - + +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 3.5 32.3 - - + -
77D TYR* 4.2 18.4 - - + +
90D LEU* 3.6 17.0 - - + +
93D ASP* 4.5 3.4 - - + -
94D TYR* 4.1 30.3 - - + +
97D THR* 4.3 11.7 - - + +
99D ASP* 3.1 23.8 + - + +
100D PRO 2.8 2.8 + - - -
101D LEU* 1.3 79.1 - - + +
103D LEU* 1.3 61.0 + - - +
105D VAL* 3.1 5.2 + - - +
106D LEU* 2.9 31.1 + - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO* 3.4 33.9 - - + +
55D ILE* 4.4 2.9 - - - +
58D MET* 3.8 18.8 - - + -
94D TYR* 3.4 39.3 - - + +
99D ASP 3.5 2.2 + - - -
100D PRO* 2.6 16.2 + - + +
102D LEU* 1.3 72.5 - - - +
104D TYR* 1.3 63.9 + - - +
106D LEU* 3.0 16.7 + - + +
107D HIS* 3.1 13.0 + - - +
115D ILE* 4.4 16.2 - - + -
117D ILE* 5.6 1.6 - - + -
123D PHE* 3.5 35.4 - - + -
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Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ALA 4.7 4.5 + - - -
5D ILE* 3.8 12.1 - - + -
58D MET* 3.3 30.7 - - + -
62D LEU* 3.6 45.3 - - + -
67D TRP* 4.0 2.0 - + - -
70D VAL* 3.8 28.5 - - + -
100D PRO 2.9 6.9 + - - +
101D LEU* 3.5 16.6 - - + +
103D LEU* 1.3 77.4 - - - +
105D VAL* 1.3 60.4 + - - +
107D HIS* 2.6 44.5 + + - -
108D PHE* 3.3 32.4 - + - -
136D SER 4.5 0.5 + - - -
139D ARG* 5.5 0.5 - - - +
140D PHE* 3.8 27.8 + + - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 4.5 13.9 - - + +
73D VAL* 3.7 32.1 - - + -
74D ILE* 3.9 26.5 - - + -
79D LEU* 4.1 2.2 - - + -
90D LEU* 3.9 18.2 - - + -
101D LEU* 3.1 25.3 + - + +
102D LEU 3.1 7.1 + - - +
104D TYR* 1.3 78.1 - - + +
106D LEU* 1.3 63.1 + - - +
108D PHE* 3.3 14.6 + - - +
109D HIS* 3.0 26.9 - - - +
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 4.1 21.4 - - + +
90D LEU* 3.4 29.4 - - + -
91D ARG* 3.6 22.0 - - + +
94D TYR* 3.9 31.4 - - + -
102D LEU 2.9 17.1 + - - +
103D LEU* 3.0 9.6 + - - +
105D VAL* 1.3 75.8 - - - +
107D HIS* 1.3 53.7 + - - +
108D PHE 2.7 0.5 + - - -
109D HIS* 2.6 33.8 + - - +
110D GLY* 3.4 7.8 + - - -
123D PHE* 3.7 39.0 - - + -
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Residues in contact with HIS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.4 35.0 - - + +
6D ALA* 4.3 11.2 + - + +
58D MET* 5.4 1.1 - - + -
103D LEU 3.1 7.7 + - - +
104D TYR* 2.6 38.6 + + - +
105D VAL 3.4 0.4 - - - -
106D LEU* 1.3 78.4 - - - +
108D PHE* 1.3 105.4 + + - +
109D HIS 3.4 0.2 + - - -
110D GLY 3.8 3.1 + - - +
113D ASN* 3.3 37.1 - - + +
114D MET 5.0 2.2 - - - -
115D ILE* 3.9 28.0 - - + -
123D PHE* 4.5 10.2 - - + -
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Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 5.8 0.2 - - + -
67D TRP* 4.2 4.7 - + - -
70D VAL* 4.6 3.6 - - + -
104D TYR* 3.3 50.0 - + - -
105D VAL* 3.3 15.4 + - + +
106D LEU 2.7 3.6 + - - -
107D HIS* 1.3 106.4 - + - +
109D HIS* 1.3 64.3 + - + +
110D GLY 3.5 0.2 - - - -
113D ASN* 3.7 10.4 - - - +
130D ARG* 3.2 21.3 - - - +
131D THR* 3.9 6.6 - - - -
132D ILE* 3.1 39.0 - - + +
133D ASN* 5.8 0.2 - - - -
136D SER* 3.1 35.2 - - - -
139D ARG* 5.6 6.5 - - - -
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Residues in contact with HIS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ILE* 4.4 8.5 - - + +
79D LEU* 3.5 45.4 - - + +
80D SER 4.4 3.6 + - - -
83D SER* 5.1 0.2 + - - -
87D PHE* 3.6 20.0 - + + -
90D LEU* 4.8 2.0 - - + -
105D VAL* 3.0 34.7 + - - +
106D LEU* 2.6 15.8 + - - +
108D PHE* 1.3 76.2 - - + +
110D GLY* 1.3 57.8 + - - -
127D PHE* 3.4 13.2 - + + -
128D GLY* 2.7 23.5 + - - -
130D ARG* 2.9 25.0 + - - +
131D THR* 2.4 31.2 + - - -
132D ILE 4.4 2.0 - - - -
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 4.2 5.6 - - - -
106D LEU 3.4 7.1 + - - -
107D HIS 3.8 4.1 + - - -
108D PHE 3.5 3.0 - - - -
109D HIS* 1.3 76.6 - - - +
111D PHE* 1.3 55.4 + - - -
112D SER 2.7 18.2 + - - -
113D ASN* 2.8 14.3 + - - -
114D MET 5.1 0.9 - - - -
123D PHE* 5.4 1.8 - - - -
125D THR* 3.9 10.3 - - - -
126D PRO 3.4 9.0 - - - -
128D GLY* 3.3 6.3 - - - -
130D ARG* 3.4 11.8 - - - -
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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