Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 2E4Y
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 ARG 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B LYS* 3.2 27.4 - - + +
51B GLY 3.2 24.2 + - - -
53B GLY 5.3 1.8 + - - -
55B GLU 4.4 4.9 + - - -
56B GLU* 3.0 42.4 + - - +
98B THR* 3.0 4.7 + - - +
99B CYS* 2.6 10.3 + - - +
100B SER* 1.3 76.1 - - - +
102B ASP* 1.3 71.2 + - - +
103B THR* 3.0 26.9 - - - +
104B TYR* 3.9 13.1 - - + +
105B ALA* 3.1 21.8 + - - +
153B VAL* 4.8 2.7 - - - -
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Residues in contact with ASP 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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100B SER 4.0 1.2 + - - -
101B ARG* 1.3 72.8 - - - +
103B THR* 1.3 96.2 + - - +
104B TYR 2.7 6.1 + - - -
105B ALA* 2.9 2.6 + - - +
106B LEU* 2.8 24.8 + - - +
152B SER* 3.7 32.9 - - - +
153B VAL* 3.9 16.3 - - - +
156B GLN* 3.8 22.0 + - + +
249B ARG* 4.5 15.6 + - - -
277B ARG* 6.1 0.2 - - - +
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Residues in contact with THR 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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101B ARG* 3.0 26.9 - - + -
102B ASP* 1.3 98.8 + - - +
104B TYR* 1.3 57.1 + - - +
106B LEU* 3.6 13.2 - - + +
107B GLU* 3.2 35.0 + - - +
156B GLN* 5.0 8.3 - - - +
249B ARG* 6.2 3.4 - - - +
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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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30B ARG* 5.0 6.9 - - - -
56B GLU* 3.7 31.6 - - + +
57B CYS* 4.0 10.2 - - - -
97B ASP* 3.4 18.5 + - + +
98B THR* 3.3 22.2 - - - -
99B CYS* 3.2 30.0 - - + -
101B ARG* 3.4 25.1 + - + +
102B ASP 2.7 4.9 + - - -
103B THR* 1.3 76.6 + - - +
105B ALA* 1.3 65.1 + - - +
106B LEU 3.1 1.1 - - - -
107B GLU* 3.1 13.8 + - + +
108B GLN* 2.9 50.9 + - + +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.9 0.8 - - + +
98B THR* 3.5 30.7 - - + -
101B ARG 3.1 5.4 + - - +
102B ASP 2.9 3.9 + - - +
104B TYR* 1.3 78.3 - - - +
106B LEU* 1.3 52.5 + - - +
108B GLN* 3.0 10.6 + - - +
109B SER* 2.6 42.6 + - - +
153B VAL* 3.2 34.3 - - + -
157B VAL* 4.3 3.1 - - + -
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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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163A LEU* 3.9 26.9 - - + +
164A PHE* 3.7 31.6 - - + -
102B ASP 2.8 14.9 + - - +
103B THR* 3.6 11.4 - - + +
105B ALA* 1.3 79.1 - - - +
107B GLU* 1.3 65.4 + - + +
109B SER* 3.1 8.8 + - - -
110B LEU* 3.1 16.1 + - - +
156B GLN* 3.3 54.7 - - + +
157B VAL* 4.4 5.7 - - - +
160B LEU* 4.5 9.5 - - + +
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Residues in contact with GLU 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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117A LEU* 4.3 26.4 - - + +
164A PHE* 5.1 10.5 - - + -
56B GLU* 4.5 12.1 - - - +
103B THR* 3.2 20.9 + - - +
104B TYR* 3.1 13.9 + - + +
106B LEU* 1.3 79.2 - - + +
108B GLN* 1.3 69.6 + - + +
110B LEU* 2.9 30.5 - - + +
111B GLU* 4.0 0.7 + - - +
114B ARG* 5.8 0.2 + - - -
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Residues in contact with GLN 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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30B ARG* 3.5 36.7 + - - +
31B ARG 5.0 2.8 - - - +
44B LEU* 4.9 2.7 - - + -
96B LEU* 3.7 34.2 - - + +
97B ASP* 3.6 20.1 + - - +
104B TYR* 2.9 51.5 + - + +
105B ALA* 3.2 9.0 - - - +
107B GLU* 1.3 79.1 - - - +
109B SER* 1.3 50.4 + - - +
111B GLU* 2.5 43.1 + - - +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.5 13.5 - - - +
105B ALA 2.6 25.9 + - - -
106B LEU* 3.3 9.0 - - - -
108B GLN* 1.3 65.8 - - - +
110B LEU* 1.3 61.7 + - - +
111B GLU 2.8 5.8 - - - -
112B PHE* 2.8 36.0 + - - +
113B VAL* 3.5 6.8 + - - +
157B VAL* 3.4 29.5 - - - +
160B LEU* 3.9 17.5 - - - +
161B LEU* 4.9 1.2 - - - +
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Residues in contact with LEU 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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110A LEU* 4.3 5.6 - - + -
113A VAL* 3.7 27.4 - - + +
114A ARG* 4.6 8.5 - - + +
117A LEU* 5.2 7.9 - - + -
164A PHE* 3.5 42.4 - - + -
106B LEU 3.1 4.2 + - - +
107B GLU* 2.9 21.0 + - + +
108B GLN 2.8 0.6 + - - -
109B SER* 1.3 76.7 - - - +
111B GLU* 1.3 61.4 + - - +
113B VAL* 3.3 13.8 - - + +
114B ARG* 3.1 40.5 + - + +
160B LEU* 3.7 25.4 - - + -
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Residues in contact with GLU 111 (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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30B ARG* 3.2 29.9 + - - +
32B GLU* 3.7 9.7 - - - +
34B LYS* 5.6 1.4 - - - -
94B HIS* 3.4 31.6 - - + +
96B LEU* 3.6 12.1 - - + -
107B GLU 4.0 0.7 + - - +
108B GLN* 2.5 22.5 + - - +
109B SER 2.8 0.2 - - - -
110B LEU* 1.3 74.4 - - - +
112B PHE* 1.3 57.3 + - + +
114B ARG* 3.7 31.1 + - - +
115B ALA* 3.1 26.6 + - - +
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Residues in contact with PHE 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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42B GLY* 3.4 22.7 - - - -
43B GLY 3.8 16.2 - - - -
44B LEU* 3.7 26.2 - - + -
94B HIS* 3.4 17.3 - + - -
96B LEU* 3.6 20.9 - - + -
109B SER* 2.8 46.3 + - - +
111B GLU* 1.3 72.0 - - - +
113B VAL* 1.3 59.8 + - - +
115B ALA* 2.9 27.1 + - - +
116B SER* 3.6 4.2 + - - -
142B ILE* 3.7 30.6 - - + +
145B VAL* 4.0 21.3 - - + -
161B LEU* 4.7 4.9 - - + -
166B ILE* 4.2 10.0 - - + +
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Residues in contact with VAL 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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110A LEU* 3.5 22.0 - - + +
109B SER 3.5 0.4 + - - -
110B LEU* 3.3 28.9 - - + +
112B PHE* 1.3 76.3 - - - +
114B ARG* 1.3 66.8 + - - +
115B ALA 3.0 0.2 - - - -
116B SER* 3.2 19.5 + - - -
117B LEU* 3.6 7.1 - - - +
160B LEU* 3.6 22.9 - - + -
161B LEU* 3.8 17.0 - - + -
164B PHE* 3.3 44.9 - - + -
166B ILE* 4.3 6.5 - - + -
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Residues in contact with ARG 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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110A LEU* 4.2 7.9 - - + -
114A ARG* 3.7 58.1 - - - +
117A LEU* 5.1 10.7 - - - +
110B LEU* 3.1 28.5 + - + +
111B GLU* 3.8 31.5 + - - +
113B VAL* 1.3 82.6 - - + +
115B ALA* 1.3 57.4 + - - +
116B SER 3.2 4.1 + - - -
117B LEU* 3.3 25.0 + - + +
139B PRO* 4.7 6.7 - - - +
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Residues in contact with ALA 115 (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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94B HIS* 5.6 3.6 - - + +
111B GLU 3.1 15.1 + - - +
112B PHE* 2.9 19.4 + - - +
114B ARG* 1.3 77.4 - - - +
116B SER* 1.3 58.3 + - - +
117B LEU 3.4 1.6 - - - -
139B PRO* 4.5 14.3 - - + +
140B LEU* 2.9 48.1 + - + +
141B LEU* 3.5 7.8 - - - +
142B ILE* 3.9 5.6 - - + -
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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