Contacts of the helix formed by residues 104 - 118 (chain B) in PDB entry 2Y4T
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B TYR* 4.2 17.0 - + - +
75B TYR* 3.7 43.7 - + - -
97B VAL* 4.1 9.9 - - + -
98B ILE* 5.0 4.0 - - - +
101B LYS* 2.9 29.8 + - + +
102B MET 4.6 2.2 - - - -
103B ASP* 1.3 74.1 - - - +
105B THR* 1.3 63.0 + - - +
106B ALA* 3.2 28.3 - - + -
107B ALA* 3.2 33.9 + - + +
108B ARG* 3.6 4.0 + - - +
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Residues in contact with THR 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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102B MET 4.5 10.3 - - - +
103B ASP 3.2 11.7 + - - +
104B PHE* 1.3 70.0 - - - +
106B ALA* 1.3 60.6 + - - +
108B ARG* 2.8 32.4 + - + +
109B LEU* 2.9 16.2 + - - +
131B VAL* 4.1 16.1 - - - +
134B SER* 3.4 33.0 - - - +
136B PRO* 4.9 4.4 - - - +
140B GLU* 3.5 20.2 + - - -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 4.1 6.5 + - - +
104B PHE* 3.2 28.4 - - + -
105B THR* 1.3 81.3 + - - +
107B ALA* 1.3 54.5 + - - +
109B LEU* 4.0 7.2 - - - +
110B GLN* 3.2 27.4 + - - +
140B GLU* 3.5 20.0 - - - +
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Residues in contact with ALA 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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75B TYR* 3.7 24.5 - - + -
94B LEU* 3.6 8.0 - - + +
97B VAL* 3.8 14.1 - - + -
98B ILE* 4.0 10.5 - - + +
104B PHE* 3.2 32.9 + - + +
105B THR 3.1 0.6 - - - -
106B ALA* 1.3 75.5 - - - +
108B ARG* 1.3 60.8 + - - +
109B LEU 3.3 0.2 - - - -
110B GLN* 3.4 2.4 + - - +
111B ARG* 3.0 27.2 + - - +
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Residues in contact with ARG 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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98B ILE* 3.3 44.5 - - + +
102B MET* 4.2 17.4 + - - +
104B PHE 3.6 2.9 + - - +
105B THR* 2.8 25.4 + - - +
107B ALA* 1.3 78.2 - - - +
109B LEU* 1.3 55.2 + - - +
111B ARG* 3.4 11.5 + - - +
112B GLY 3.1 20.4 + - - -
127B ASP* 3.4 32.0 + - - +
130B LYS* 3.4 51.9 - - - +
131B VAL* 4.1 14.8 - - + +
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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
----------------------------------------------------------
105B THR 2.9 13.5 + - - +
106B ALA* 4.0 7.0 - - - +
108B ARG* 1.3 75.4 - - - +
110B GLN* 1.3 64.7 + - - +
112B GLY* 3.0 12.6 + - - +
113B HIS* 3.0 38.7 + - + +
127B ASP* 5.5 0.7 - - - -
128B PHE* 3.9 16.8 - - + -
131B VAL* 3.8 15.6 - - + +
140B GLU* 3.8 41.1 - - + +
143B GLU* 4.5 9.9 - - + +
144B ALA* 3.7 33.4 - - + +
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Residues in contact with GLN 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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75B TYR* 3.9 20.6 + - + +
79B THR* 5.3 6.9 - - + +
82B LEU* 3.8 29.2 - - + +
94B LEU* 3.9 14.4 - - + +
106B ALA 3.2 19.3 + - - +
107B ALA* 3.6 8.3 - - - +
108B ARG 3.3 0.2 - - - -
109B LEU* 1.3 76.1 - - - +
111B ARG* 1.3 60.7 + - - +
113B HIS* 3.7 13.9 + - - +
114B LEU* 3.3 21.5 + - - +
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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
----------------------------------------------------------
91B LEU* 4.9 6.7 - - + -
94B LEU* 3.7 22.6 - - + +
95B THR* 3.2 46.3 - - - +
98B ILE* 3.5 20.8 - - + +
107B ALA 3.0 13.8 + - - +
108B ARG* 3.5 17.1 - - - +
109B LEU 3.1 0.2 - - - -
110B GLN* 1.3 74.3 - - - +
112B GLY* 1.3 54.9 + - - +
114B LEU* 3.4 2.1 + - + +
115B LEU* 2.7 55.2 + - + +
123B GLU 5.7 0.2 + - - -
127B ASP* 2.7 36.8 + - - -
130B LYS* 6.1 0.6 - - - +
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Residues in contact with GLY 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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108B ARG 3.1 8.0 + - - -
109B LEU 3.0 7.4 + - - -
111B ARG* 1.3 75.6 - - - +
113B HIS* 1.3 52.0 + - - +
115B LEU* 3.2 4.9 + - - +
116B LEU* 2.8 36.2 + - - +
124B ALA* 3.8 3.7 - - - +
127B ASP* 3.9 19.7 + - - -
128B PHE* 3.7 20.8 - - - -
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Residues in contact with HIS 113 (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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109B LEU* 3.0 52.2 + - + +
110B GLN* 3.9 18.6 - - - +
112B GLY* 1.3 75.7 - - - +
114B LEU* 1.3 61.6 + - - +
116B LEU* 3.4 2.3 + - - +
117B LYS* 3.0 33.8 + - - +
128B PHE* 3.9 2.0 - + - -
143B GLU* 3.2 40.5 + - + +
147B GLN* 3.1 42.6 + - + +
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Residues in contact with LEU 114 (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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82B LEU* 3.6 14.4 - - + -
87B SER* 3.6 15.7 - - - +
90B ALA* 3.8 5.6 - - + -
91B LEU* 3.6 42.0 - - + +
94B LEU* 3.7 18.8 - - + -
110B GLN 3.3 12.7 + - - +
111B ARG* 3.7 6.3 - - - +
112B GLY 3.3 0.2 - - - -
113B HIS* 1.3 78.1 - - - +
115B LEU* 1.3 56.9 + - - +
117B LYS* 2.9 13.8 + - - +
118B GLN* 2.9 40.3 + - - +
186B TRP* 3.4 32.1 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.7 26.9 - - + -
111B ARG* 2.7 39.6 + - + +
112B GLY* 3.7 3.6 - - - +
114B LEU* 1.3 73.4 - - + +
116B LEU* 1.3 60.2 + - - +
118B GLN* 3.4 13.4 + - - +
119B GLY 3.3 3.1 + - - -
120B LYS* 3.2 38.5 + - + +
123B GLU* 4.2 36.3 - - + +
124B ALA* 4.1 13.0 - - + +
127B ASP* 3.3 26.9 - - - +
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Residues in contact with LEU 116 (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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112B GLY 2.8 19.6 + - - +
113B HIS 3.8 4.3 - - - +
115B LEU* 1.3 70.6 - - - +
117B LYS* 1.3 60.9 + - - +
119B GLY* 3.0 14.7 + - - +
120B LYS 5.0 0.4 - - - +
121B LEU* 3.8 21.3 - - + -
124B ALA* 3.8 12.3 - - + +
128B PHE* 4.1 5.6 - - + -
147B GLN* 3.3 46.9 - - - +
150B LYS* 4.6 2.0 - - + -
151B SER* 3.8 28.5 - - - +
154B MET* 4.7 2.7 - - + -
183B VAL* 4.1 21.3 - - + -
184B CYS* 3.3 23.5 - - - -
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Residues in contact with LYS 117 (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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82B LEU* 4.7 7.3 + - - +
113B HIS* 3.0 21.9 + - - +
114B LEU* 2.9 15.3 + - - +
116B LEU* 1.3 74.6 - - - +
118B GLN* 1.3 58.5 + - - +
119B GLY 3.1 0.2 - - - -
183B VAL 4.0 12.6 - - - +
184B CYS 3.1 9.5 - - - -
185B VAL* 3.7 24.7 - - + -
186B TRP* 2.7 74.8 + - + -
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Residues in contact with GLN 118 (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 SER* 3.4 42.6 + - - +
88B LYS* 4.6 3.6 - - - +
91B LEU* 3.3 29.5 - - - +
114B LEU* 2.9 22.4 + - + +
115B LEU* 3.4 12.8 - - - +
117B LYS* 1.3 75.7 - - - +
119B GLY* 1.3 61.8 + - - +
120B LYS* 2.9 38.7 + - + +
186B TRP* 3.7 10.0 - - + +
187B ASP* 3.3 22.4 - - - +
189B GLU* 5.4 1.2 - - - +
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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