Contacts of the helix formed by residues 103 - 115 (chain B) in PDB entry 1W4Z
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 ALA 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.3 1.6 - - - +
101B GLU 3.3 5.9 + - - +
102B LEU* 1.3 76.5 - - - +
104B ASP* 1.3 66.0 + - - +
105B GLU* 4.1 9.6 - - + +
106B LEU* 3.0 28.0 + - + +
107B TRP* 3.1 11.0 + - - +
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Residues in contact with ASP 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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67A VAL* 3.8 14.6 - - + +
116A THR* 5.4 0.2 - - - +
119A PHE* 4.3 10.9 - - - -
120A ARG* 2.7 54.0 + - - +
123A LYS* 3.7 12.8 + - - +
102B LEU 3.3 4.3 + - - -
103B ALA* 1.3 72.0 - - - +
105B GLU* 1.3 60.6 + - + +
107B TRP* 3.4 3.8 + - - +
108B LEU* 3.0 34.7 + - - +
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Residues in contact with GLU 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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103B ALA* 3.1 6.6 - - + +
104B ASP* 1.3 79.2 - - + +
106B LEU* 1.3 60.6 + - - +
108B LEU* 3.2 18.8 + - - +
109B ASP* 2.8 30.2 + - - +
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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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93B ARG* 3.3 38.8 - - - +
95B GLY* 4.9 1.8 - - - -
96B GLY 4.0 26.5 - - - +
102B LEU* 4.2 17.5 - - + -
103B ALA* 3.0 21.2 + - + +
105B GLU* 1.3 76.0 - - - +
107B TRP* 1.3 67.3 + - - +
109B ASP* 3.2 2.9 + - - +
110B VAL* 3.0 36.5 + - + +
156B PRO* 5.5 1.1 - - + -
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Residues in contact with TRP 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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115A LEU* 3.9 27.6 - - + -
116A THR* 3.0 34.4 + - + +
119A PHE* 3.5 70.2 - + + -
167A PHE* 3.8 17.5 - + - -
102B LEU* 4.2 6.4 - - + +
103B ALA 3.1 7.9 + - - +
104B ASP* 3.6 6.5 - - - +
106B LEU* 1.3 80.0 - - - +
108B LEU* 1.3 68.5 - - + +
110B VAL* 4.0 0.9 - - - +
111B VAL* 3.1 34.9 + - + +
155B ALA* 4.7 0.2 - - + -
156B PRO* 3.5 42.2 - - + -
159B ALA* 3.8 20.4 - - + -
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Residues in contact with LEU 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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112A GLU* 4.1 15.9 - - - +
116A THR* 4.3 14.8 - - + +
120A ARG* 3.7 19.7 - - - +
104B ASP* 3.0 36.3 + - - +
105B GLU* 3.7 20.9 - - - +
106B LEU 3.2 0.4 - - - -
107B TRP* 1.3 80.7 - - + +
109B ASP* 1.3 58.3 + - - +
111B VAL* 3.9 2.9 - - + +
112B GLU* 2.9 33.1 + - - +
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Residues in contact with ASP 109 (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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65B ARG* 2.9 42.6 + - - -
93B ARG* 2.7 40.1 + - - +
105B GLU 2.8 17.7 + - - +
106B LEU* 3.9 2.9 - - - +
107B TRP 3.2 0.2 - - - -
108B LEU* 1.3 76.6 - - - +
110B VAL* 1.3 64.6 + - - +
112B GLU* 3.8 5.3 - - - +
113B THR* 2.8 31.7 + - - -
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Residues in contact with VAL 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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93B ARG* 3.7 31.9 - - - +
94B PRO 3.9 0.4 - - - +
95B GLY* 3.8 21.5 - - - -
106B LEU* 3.0 20.6 + - + +
107B TRP 4.0 2.7 - - - +
109B ASP* 1.3 73.5 - - - +
111B VAL* 1.3 58.7 + - - +
114B ASN* 2.8 45.8 + - - +
156B PRO* 3.5 39.3 - - + +
157B TYR* 4.0 4.9 - - + +
160B SER* 3.7 9.2 - - - +
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Residues in contact with VAL 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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111A VAL* 3.9 27.6 - - + -
115A LEU* 4.5 7.2 - - + -
116A THR* 4.9 3.8 - - - +
107B TRP* 3.1 48.0 + - + +
108B LEU* 4.0 3.8 - - + +
110B VAL* 1.3 76.0 - - + +
112B GLU* 1.3 59.8 + - - +
115B LEU* 2.9 38.5 + - + -
116B THR* 3.0 13.1 + - - +
156B PRO* 4.7 6.3 - - + +
160B SER* 4.2 16.8 - - - +
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Residues in contact with GLU 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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108A LEU* 5.2 5.5 - - + +
64B VAL 4.6 1.7 - - - +
65B ARG* 3.7 33.5 - - + +
108B LEU 2.9 20.0 + - - +
109B ASP* 4.0 5.8 - - - +
111B VAL* 1.3 77.4 - - - +
113B THR* 1.3 57.7 + - - +
116B THR* 3.6 12.4 - - + +
117B GLY* 3.1 24.4 + - - -
120B ARG* 3.1 32.8 + - - +
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Residues in contact with THR 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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64B VAL* 3.9 12.5 - - + +
65B ARG* 3.4 24.2 + - - -
91B ALA 4.2 4.9 - - - +
92B GLY* 4.3 11.7 - - - +
93B ARG* 3.9 15.2 - - + +
109B ASP* 2.8 24.2 + - - -
110B VAL 3.9 0.2 - - - -
112B GLU* 1.3 79.2 - - - +
114B ASN* 1.3 76.0 + - - +
115B LEU 3.7 0.2 + - - -
117B GLY* 3.7 13.5 - - - -
118B VAL* 4.5 0.7 + - - +
1262B NAP 3.9 25.6 - - + +
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Residues in contact with ASN 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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91B ALA 4.7 5.1 - - - +
92B GLY* 3.1 8.6 - - - -
93B ARG* 2.7 49.8 + - - +
110B VAL* 2.8 24.3 + - - +
113B THR* 1.3 74.7 - - - +
115B LEU* 1.3 58.2 + - - +
118B VAL* 3.2 15.1 - - - +
157B TYR* 3.9 15.8 - - - -
160B SER* 3.3 24.3 + - - +
161B LYS* 4.2 17.4 + - + +
164B VAL* 3.2 19.6 - - - +
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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
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107A TRP* 3.9 25.3 - - + -
111A VAL* 4.5 11.4 - - + -
115A LEU* 4.3 17.3 - - + -
159A ALA* 4.1 9.6 - - + +
111B VAL* 2.9 28.2 + - + +
114B ASN* 1.3 78.4 - - - +
116B THR* 1.3 67.7 + - - +
117B GLY 3.1 0.9 - - - -
118B VAL* 3.1 14.9 + - + +
119B PHE 3.3 7.6 + - - -
160B SER* 3.8 16.6 - - - +
163B GLY* 3.5 40.6 - - - +
164B VAL* 3.7 7.4 - - + +
167B PHE* 4.9 3.1 - - + -
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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