Contacts of the helix formed by residues 103 - 116 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TRP* 5.3 2.6 - - - -
99A GLN 3.7 17.6 + - - -
100A ALA 3.9 4.4 + - - -
101A VAL 3.5 0.4 - - - -
102A LEU* 1.3 82.0 - - - +
104A ARG* 1.3 66.2 + - - +
105A GLU* 3.5 15.4 + - - +
106A ALA* 3.0 23.6 + - - +
107A VAL* 2.9 21.0 + - - +
184A PRO* 3.8 1.1 - - - -
185A LEU 3.6 13.2 - - - -
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Residues in contact with ARG 104 (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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103A SER* 1.3 74.2 - - - +
105A GLU* 1.3 72.6 + - + +
107A VAL* 3.8 1.5 - - - +
108A SER* 2.9 34.6 + - - -
111A ARG* 5.5 0.5 + - - -
183A GLU* 4.0 11.9 + - - +
184A PRO* 3.5 44.7 - - + +
185A LEU 4.1 2.2 + - - -
187A ALA* 6.3 0.4 - - - +
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Residues in contact with GLU 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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26A GLN* 3.3 44.8 + - + +
30A SER* 4.6 5.6 - - - +
71A TRP* 4.0 10.1 - - + +
103A SER* 3.6 17.6 + - - +
104A ARG* 1.3 91.4 + - + +
106A ALA* 1.3 61.7 + - - +
108A SER* 3.4 6.6 + - - -
109A LEU* 3.1 23.6 + - - +
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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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71A TRP* 3.6 27.4 - - + -
100A ALA 3.7 6.3 - - - +
101A VAL* 3.3 31.2 - - - +
103A SER* 3.0 18.4 + - - +
105A GLU* 1.3 78.8 - - - +
107A VAL* 1.3 63.8 + - - +
109A LEU* 3.3 4.3 + - - +
110A PHE* 3.1 21.0 + - - +
127A TYR* 4.7 3.1 + - - -
174A LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 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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101A VAL 4.3 0.2 - - - +
102A LEU* 3.8 19.1 - - - +
103A SER 2.9 16.9 + - - +
104A ARG* 4.2 3.1 - - - +
106A ALA* 1.3 73.2 - - - +
108A SER* 1.3 66.0 + - - +
110A PHE* 3.2 6.1 + - - +
111A ARG* 2.8 46.7 + - - +
174A LEU* 3.9 17.9 - - + -
177A ILE* 3.8 31.6 - - + -
178A THR* 3.7 22.4 - - - +
184A PRO* 5.5 0.7 - - + -
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Residues in contact with SER 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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26A GLN* 6.3 0.4 - - - -
30A SER* 6.2 0.5 - - - -
104A ARG* 2.9 23.4 + - - -
105A GLU* 3.7 7.9 - - - -
106A ALA 3.3 0.2 - - - -
107A VAL* 1.3 77.1 - - - +
109A LEU* 1.3 57.7 + - - +
111A ARG* 3.3 18.6 + - - +
112A MSE 2.9 39.4 + - - +
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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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29A LEU* 4.6 9.0 - - + -
64A ILE* 4.1 31.2 - - + -
67A LEU* 4.7 7.2 - - + -
68A VAL* 3.7 29.4 - - + -
71A TRP* 3.9 13.5 - - + -
105A GLU 3.1 16.2 + - - +
106A ALA 3.7 5.2 - - - +
107A VAL 3.1 0.2 - - - -
108A SER* 1.3 75.3 - - - +
110A PHE* 1.3 64.7 - - - +
112A MSE 3.2 25.8 + - - +
113A LEU* 3.1 36.4 + - + +
123A PHE* 5.5 0.4 - - + -
127A TYR* 3.8 17.3 - - + -
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Residues in contact with PHE 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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106A ALA 3.1 11.4 + - - +
107A VAL 3.5 7.6 - - - +
109A LEU* 1.3 77.6 - - - +
111A ARG* 1.3 58.7 + - - +
113A LEU* 3.2 6.0 + - + +
114A ALA* 2.8 40.7 + - + +
127A TYR* 3.6 30.6 + + - +
174A LEU* 3.9 35.9 - - + -
175A ARG* 5.9 1.6 - - - -
178A THR* 3.3 37.5 - - + -
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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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104A ARG 5.5 0.4 + - - -
107A VAL* 2.8 31.2 + - - +
108A SER* 3.6 26.9 + - - +
110A PHE* 1.3 79.5 - - - +
112A MSE 1.3 60.1 + - - +
114A ALA* 3.2 8.4 + - + +
115A SER* 2.7 38.4 + - - +
177A ILE* 3.1 28.7 + - - +
178A THR* 3.1 30.2 + - + -
180A GLY* 5.1 0.8 - - - +
184A PRO* 6.1 0.8 - - - +
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Residues in contact with MSE 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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29A LEU* 3.8 37.9 - - + +
33A GLY* 4.5 8.5 - - - -
34A ALA* 4.1 24.2 - - - +
108A SER* 2.9 24.8 + - - +
109A LEU* 3.4 25.1 - - + +
111A ARG* 1.3 75.9 - - - +
113A LEU* 1.3 63.8 + - + +
115A SER* 3.2 13.5 + - - -
116A ASP* 3.3 16.8 + - - +
119A LEU* 3.6 19.2 - - + +
123A PHE* 5.5 3.6 - - - -
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Residues in contact with LEU 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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64A ILE* 5.7 0.2 - - + -
109A LEU* 3.1 22.4 + - + +
110A PHE* 3.7 7.9 - - + +
112A MSE 1.3 77.2 - - + +
114A ALA* 1.3 64.3 + - - +
115A SER 3.1 0.5 + - - -
116A ASP 3.5 4.9 + - - -
119A LEU* 3.7 34.1 - - + +
120A ARG* 2.8 43.4 + - + +
123A PHE* 4.0 19.5 - - + -
124A LEU* 5.0 9.0 - - + -
127A TYR* 3.6 49.4 - - + -
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Residues in contact with ALA 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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110A PHE* 2.8 34.6 + - + +
111A ARG* 3.2 10.5 + - + +
113A LEU* 1.3 77.5 - - - +
115A SER* 1.3 58.5 + - - +
120A ARG* 3.1 17.5 + - - +
178A THR* 5.8 3.1 - - + -
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Residues in contact with SER 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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111A ARG* 2.7 30.1 + - - +
112A MSE 3.6 7.0 - - - -
113A LEU 3.0 0.4 - - - -
114A ALA* 1.3 79.5 - - - +
116A ASP* 1.3 59.2 + - - +
120A ARG* 4.4 0.7 - - - -
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Residues in contact with ASP 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 MSE 3.3 12.3 + - - +
113A LEU 3.5 8.2 + - - +
114A ALA 3.5 0.8 + - - -
115A SER* 1.3 82.2 - - - +
117A ALA* 1.3 57.2 + - - +
118A ASP* 2.9 22.9 + - - +
119A LEU* 3.1 33.9 + - + +
120A ARG* 3.0 26.4 + - - -
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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