Contacts of the helix formed by residues 104 - 118 (chain A) in PDB entry 2Y4U
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 PHE 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 4.4 13.9 - + - -
75A TYR* 3.9 38.4 - + - -
97A VAL* 4.2 11.4 - - + +
98A ILE* 5.2 3.6 - - - +
101A LYS* 2.9 40.4 + - + +
102A MSE 4.8 1.5 - - - +
103A ASP* 1.3 76.8 - - - +
105A THR* 1.3 64.8 + - - +
106A ALA* 3.5 29.2 - - + -
107A ALA* 3.6 24.3 - - + +
108A ARG* 4.2 3.5 + - - +
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Residues in contact with THR 105 (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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102A MSE 5.3 1.6 - - - +
103A ASP 2.9 18.8 + - - +
104A PHE* 1.3 70.1 - - - +
106A ALA* 1.3 65.7 + - - +
107A ALA 2.8 6.9 + - - -
108A ARG* 2.9 25.8 + - + +
109A LEU* 3.0 10.7 + - - +
130A LYS 5.7 1.3 - - - +
131A VAL* 4.1 18.5 - - + +
134A SER* 5.6 3.4 - - - -
135A ASN* 3.5 44.8 + - + +
140A GLU* 3.7 18.5 + - - -
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Residues in contact with ALA 106 (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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75A TYR* 5.2 4.3 - - - +
104A PHE* 3.5 26.2 - - + -
105A THR* 1.3 80.4 + - - +
107A ALA* 1.3 50.9 + - - +
109A LEU* 3.2 17.2 - - + +
110A GLN* 2.8 37.1 + - + +
140A GLU* 3.9 18.5 + - - +
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Residues in contact with ALA 107 (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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75A TYR* 4.5 7.0 - - + -
94A LEU* 4.4 6.4 - - + +
97A VAL* 3.7 29.8 - - + -
98A ILE* 4.0 11.3 - - + +
104A PHE* 3.6 24.8 + - + +
105A THR 2.8 1.0 + - - -
106A ALA* 1.3 76.4 - - - +
108A ARG* 1.3 59.2 + - - +
109A LEU 3.1 1.3 - - - -
110A GLN* 3.1 10.1 + - - +
111A ARG* 2.8 28.4 + - - +
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Residues in contact with ARG 108 (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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98A ILE* 3.4 46.8 - - + +
102A MSE 3.9 28.5 + - - +
104A PHE 4.2 3.0 + - - +
105A THR* 2.9 22.1 + - - +
107A ALA* 1.3 74.7 - - - +
109A LEU* 1.3 57.9 + - - +
111A ARG* 3.5 5.5 + - - +
112A GLY* 3.0 22.9 + - - -
127A ASP* 3.2 50.4 + - - +
128A PHE* 5.8 0.3 - - - -
130A LYS* 4.0 34.1 - - - +
131A VAL* 3.9 11.8 - - + +
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Residues in contact with LEU 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 THR 3.0 10.8 + - - +
106A ALA* 3.2 22.2 - - + +
108A ARG* 1.3 74.9 - - - +
110A GLN* 1.3 76.1 + - - +
112A GLY* 3.2 3.0 + - - -
113A HIS* 3.1 34.0 + - + +
128A PHE* 4.5 9.3 - - + -
131A VAL* 3.8 17.4 - - + +
140A GLU* 4.3 24.0 - - + +
143A GLU* 3.8 25.1 - - + +
144A ALA* 4.2 31.4 - - + +
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Residues in contact with GLN 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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75A TYR* 3.9 24.3 + - + +
79A THR* 5.6 3.0 - - + +
82A LEU* 4.2 21.2 - - + +
94A LEU* 3.9 20.9 - - + +
106A ALA* 2.8 18.8 + - + +
107A ALA* 3.1 9.4 + - - +
109A LEU* 1.3 90.9 - - - +
111A ARG* 1.3 62.4 + - - +
113A HIS* 3.1 25.6 + - - +
114A LEU* 3.1 13.3 + - - +
143A GLU* 5.4 0.2 - - - +
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Residues in contact with ARG 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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91A LEU* 5.3 5.2 - - + +
94A LEU* 3.7 18.2 - - + +
95A THR* 3.3 44.0 - - + +
98A ILE* 3.3 34.2 - - + +
99A GLN* 6.1 0.6 - - - +
107A ALA 2.8 15.2 + - - +
108A ARG* 3.6 12.0 - - - +
109A LEU 3.3 0.2 - - - -
110A GLN* 1.3 71.6 - - - +
112A GLY* 1.3 63.6 + - - +
114A LEU* 3.0 6.3 + - + +
115A LEU* 2.9 42.8 + - + +
123A GLU 5.7 0.6 + - - -
127A ASP* 2.7 30.9 + - - +
130A LYS* 6.1 0.8 - - - +
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Residues in contact with GLY 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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108A ARG 3.0 15.5 + - - -
109A LEU 3.2 4.6 + - - -
111A ARG* 1.3 75.4 - - - +
113A HIS* 1.3 62.1 - - - +
115A LEU* 3.5 13.0 + - - +
116A LEU* 3.0 22.7 + - - +
124A ALA* 3.9 4.8 - - - +
127A ASP* 4.5 9.2 + - - -
128A PHE* 3.8 22.5 - - - -
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Residues in contact with HIS 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 LEU* 3.1 38.5 + - + +
110A GLN* 3.1 22.5 + - - +
112A GLY* 1.3 73.2 - - - +
114A LEU* 1.3 53.2 + - - +
116A LEU* 2.9 6.8 + - - +
117A LYS* 2.7 47.3 + - - +
128A PHE* 4.0 3.0 - + - -
143A GLU* 2.8 31.4 + - + +
147A GLN* 2.9 45.2 + - + -
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Residues in contact with LEU 114 (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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82A LEU* 4.1 8.7 - - + -
87A SER* 3.9 7.0 - - - +
90A ALA* 3.8 13.0 - - + -
91A LEU* 3.5 39.0 - - + +
94A LEU* 3.9 14.1 - - + -
110A GLN 3.1 7.9 + - - +
111A ARG* 3.0 9.8 + - + +
113A HIS* 1.3 77.9 - - - +
115A LEU* 1.3 51.6 + - + +
116A LEU 2.8 1.7 + - - -
117A LYS* 2.8 10.6 + - - +
118A GLN* 2.6 57.4 + - + +
186A TRP* 3.6 35.0 - - + -
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Residues in contact with LEU 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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91A LEU* 3.9 26.5 - - + -
111A ARG* 2.9 41.1 + - + +
112A GLY* 3.7 8.1 - - - +
114A LEU* 1.3 71.7 - - + +
116A LEU* 1.3 58.0 + - - +
118A GLN* 3.8 9.6 - - - +
119A GLY 3.2 1.6 + - - -
120A LYS* 2.8 45.9 + - + +
123A GLU* 4.0 33.0 - - + +
124A ALA* 3.7 12.6 - - + +
127A ASP* 3.5 24.9 - - - +
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Residues in contact with LEU 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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112A GLY 3.0 12.1 + - - +
113A HIS* 2.9 10.3 + - - +
114A LEU 2.8 0.4 + - - -
115A LEU* 1.3 75.8 - - - +
117A LYS* 1.3 62.4 + - + +
118A GLN 2.9 1.3 - - - -
119A GLY* 2.6 22.3 + - - +
121A LEU* 3.8 25.1 - - + -
124A ALA* 4.1 6.5 - - + +
128A PHE* 4.6 9.2 - - + -
147A GLN* 3.6 30.5 - - - +
150A LYS* 5.0 4.9 - - + -
151A SER* 3.9 27.1 - - - +
154A MSE 4.9 0.2 - - + -
183A VAL* 3.6 31.4 - - + +
184A CYS* 3.3 12.0 - - - +
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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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82A LEU* 5.3 8.8 + - - +
113A HIS* 2.7 31.1 + - - +
114A LEU* 3.4 8.7 - - - +
116A LEU* 1.3 72.8 - - + +
118A GLN* 1.3 57.6 + - - +
183A VAL 3.9 13.0 - - - +
184A CYS* 3.2 12.0 - - - +
185A VAL* 4.1 14.1 - - + +
186A TRP* 2.8 80.8 + - + -
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Residues in contact with GLN 118 (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 SER* 3.8 27.3 + - - +
88A LYS* 5.1 2.7 - - - +
91A LEU* 3.6 27.9 - - - +
114A LEU* 2.6 46.6 + - + +
115A LEU* 3.7 9.8 - - - +
117A LYS* 1.3 73.4 - - - +
119A GLY* 1.3 60.9 + - - +
120A LYS* 3.3 32.8 + - + +
186A TRP 3.8 10.9 - - - +
187A ASP* 3.2 22.5 - - - +
189A GLU* 5.1 0.7 - - - +
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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