Contacts of the helix formed by residues 103 - 116 (chain B) in PDB entry 3CWR
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 SER 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B TRP* 5.5 2.3 - - - -
99B GLN 3.6 16.9 + - - -
100B ALA 3.9 4.7 + - - -
101B VAL 3.6 0.4 - - - -
102B LEU* 1.3 81.6 - - - +
104B ARG* 1.3 65.8 + - - +
105B GLU* 3.5 14.4 + - - +
106B ALA* 3.0 23.6 + - - +
107B VAL* 2.9 21.7 + - - +
184B PRO* 3.8 1.3 - - - -
185B LEU 3.6 12.6 - - - -
186B PRO* 6.2 0.2 - - - -
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Residues in contact with ARG 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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103B SER* 1.3 74.0 - - - +
105B GLU* 1.3 72.6 + - + +
107B VAL* 3.9 1.4 - - - +
108B SER* 2.9 34.4 + - - -
183B GLU* 4.1 14.1 + - - +
184B PRO* 3.5 47.7 + - + +
185B LEU 4.1 2.4 + - - -
187B ALA* 6.3 0.8 - - - +
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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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26B GLN* 3.3 45.3 + - + +
30B SER* 4.6 6.5 + - - +
71B TRP* 3.9 9.4 - - + +
103B SER* 3.7 13.7 + - - +
104B ARG* 1.3 95.0 + - - +
106B ALA* 1.3 63.2 + - - +
108B SER* 3.7 5.7 - - - -
109B LEU* 3.1 23.4 + - - +
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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
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71B TRP* 3.6 24.2 - - + -
100B ALA 3.6 9.0 - - - +
101B VAL* 3.3 32.3 - - - +
103B SER* 3.0 18.6 + - - +
105B GLU* 1.3 79.1 - - - +
107B VAL* 1.3 62.8 + - - +
109B LEU* 3.3 4.2 + - - +
110B PHE* 3.1 21.7 + - - +
127B TYR* 4.7 2.9 + - - -
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Residues in contact with VAL 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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101B VAL 4.2 0.2 - - - +
102B LEU* 3.9 18.8 - - - +
103B SER 2.9 20.6 + - - +
104B ARG* 4.4 2.7 - - - +
106B ALA* 1.3 73.2 - - - +
108B SER* 1.3 66.9 + - - +
110B PHE* 3.2 5.7 + - + +
111B ARG* 2.9 44.5 + - - +
174B LEU* 3.9 20.0 - - + -
177B ILE* 3.8 28.0 - - + -
178B THR* 3.7 24.0 - - - +
184B PRO* 5.4 0.7 - - + -
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Residues in contact with SER 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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104B ARG* 2.9 23.4 + - - -
105B GLU* 3.7 6.7 - - - -
106B ALA 3.3 0.2 - - - -
107B VAL* 1.3 77.9 - - - +
109B LEU* 1.3 57.1 + - - +
111B ARG* 3.3 19.4 + - - +
112B MSE 2.9 38.5 + - - +
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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
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29B LEU* 4.5 9.4 - - + -
64B ILE* 4.1 26.2 - - + -
67B LEU* 4.6 9.6 - - + -
68B VAL* 3.7 30.1 - - + -
71B TRP* 3.8 15.3 - - + -
105B GLU 3.1 17.0 + - - +
106B ALA 3.7 4.7 - - - +
108B SER* 1.3 73.3 - - - +
110B PHE* 1.3 66.1 + - - +
112B MSE 3.2 25.7 + - - +
113B LEU* 3.1 33.9 + - + +
123B PHE* 5.6 0.7 - - + -
127B TYR* 3.8 18.6 - - + -
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Residues in contact with PHE 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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106B ALA 3.1 12.0 + - - +
107B VAL* 3.2 10.5 + - - +
109B LEU* 1.3 77.7 - - - +
111B ARG* 1.3 59.6 + - - +
113B LEU* 3.2 5.4 + - + +
114B ALA* 2.9 40.5 + - + +
127B TYR* 3.6 30.9 + + - +
174B LEU* 3.9 33.0 - - + -
175B ARG* 6.0 1.1 - - - -
178B THR* 3.3 38.6 - - + -
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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
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107B VAL* 2.9 32.2 + - - +
108B SER* 3.6 25.0 + - - +
109B LEU 3.2 0.2 - - - -
110B PHE* 1.3 80.0 - - - +
112B MSE 1.3 59.3 + - - +
114B ALA* 3.3 7.0 + - + +
115B SER* 2.7 40.0 + - - +
177B ILE* 3.1 29.1 + - - +
178B THR* 3.1 32.2 + - + +
180B GLY* 5.2 0.6 - - - +
184B PRO* 5.8 2.2 - - - +
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Residues in contact with MSE 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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29B LEU* 3.9 29.2 - - + +
33B GLY* 4.6 7.4 - - - -
34B ALA* 3.9 30.5 - - - +
108B SER* 2.9 23.3 + - - +
109B LEU* 3.4 25.1 - - + +
111B ARG* 1.3 77.9 - - - +
113B LEU* 1.3 62.7 + - + +
115B SER* 3.3 13.3 + - - -
116B ASP* 3.4 16.6 + - - +
119B LEU* 3.5 19.2 - - + +
123B PHE* 5.4 4.9 - - - -
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Residues in contact with LEU 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 ILE* 5.7 0.4 - - + -
109B LEU* 3.1 17.3 + - + +
110B PHE* 3.7 6.3 - - + +
112B MSE 1.3 76.5 - - + +
114B ALA* 1.3 61.4 + - - +
115B SER 3.1 2.8 + - - -
116B ASP 3.5 4.5 + - - -
119B LEU* 3.8 32.5 - - + +
120B ARG* 2.9 42.5 + - + +
123B PHE* 4.0 21.8 - - + -
124B LEU* 5.0 9.0 - - + -
127B TYR* 3.5 54.5 - - + -
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Residues in contact with ALA 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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110B PHE* 2.9 35.1 + - + +
111B ARG* 3.3 9.2 + - + +
113B LEU* 1.3 76.2 - - - +
115B SER* 1.3 58.8 + - - +
120B ARG* 3.1 16.9 + - - +
178B THR* 5.8 3.1 - - + -
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Residues in contact with SER 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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111B ARG* 2.7 28.9 + - - +
112B MSE 3.7 7.0 - - - -
113B LEU 3.1 0.4 - - - -
114B ALA* 1.3 79.8 - - - +
116B ASP* 1.3 59.6 + - - +
117B ALA 4.3 0.4 - - - -
120B ARG* 4.4 0.7 - - - -
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Residues in contact with ASP 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 MSE 3.4 12.9 + - - +
113B LEU 3.5 2.8 + - - +
114B ALA 3.5 0.8 + - - -
115B SER* 1.3 81.7 - - - +
117B ALA* 1.3 65.3 + - - +
118B ASP* 2.9 24.1 + - - +
119B LEU* 3.0 31.3 + - + +
120B ARG* 3.0 26.3 + - - +
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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