Contacts of the helix formed by residues 103 - 114 (chain G) in PDB entry 3WBR
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102G GLN* 1.3 74.8 + - - +
104G TRP* 1.3 56.8 + - - +
105G THR* 3.5 7.7 + - - -
106G LYS* 3.2 30.6 + - - +
107G SER* 2.7 34.7 + - - -
141G PHE* 3.6 1.8 - - - -
198G CYS 3.6 13.0 - - - -
199G HIS* 4.1 20.2 + - - -
200G VAL 4.4 0.9 - - - -
201G PRO* 4.1 3.6 - - - +
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Residues in contact with TRP 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C VAL* 3.7 27.1 - - + -
103G SER* 1.3 71.0 - - - +
105G THR* 1.3 72.8 + - - +
107G SER* 3.2 2.9 + - - -
108G GLN* 2.9 36.6 + - + -
118G LEU* 3.6 15.2 - - + +
141G PHE* 3.3 33.8 - + + -
142G LEU 2.8 25.8 + - - -
143G GLY* 4.1 17.0 - - - -
144G LEU 4.0 4.8 + - - -
145G SER* 3.7 26.5 - - - -
180G CYS* 3.2 35.4 - - + -
198G CYS* 3.0 19.8 + - + +
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Residues in contact with THR 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G SER* 3.3 7.2 + - - -
104G TRP* 1.3 94.2 - - - +
106G LYS* 1.3 67.5 + - + +
108G GLN* 3.3 5.4 + - - +
109G LYS* 3.0 27.9 + - + +
178G GLU* 5.5 3.5 + - - -
198G CYS* 4.8 2.5 + - - +
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Residues in contact with LYS 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 5.4 8.3 + - - -
102G GLN* 4.0 28.1 + - + +
103G SER* 3.2 22.9 + - - +
105G THR* 1.3 82.8 - - + +
107G SER* 1.3 60.9 + - - +
109G LYS* 3.3 36.9 + - - +
110G ASN* 2.8 37.8 + - - +
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLN* 3.5 16.4 + - - +
103G SER 2.7 24.3 + - - -
104G TRP* 3.4 7.9 - - - -
106G LYS* 1.3 77.2 - - - +
108G GLN* 1.3 56.2 + - - +
110G ASN* 3.2 11.1 + - - +
111G CYS* 2.9 31.4 + - - -
118G LEU* 3.8 10.5 - - - -
141G PHE* 3.8 5.0 - - - -
202G GLN 4.2 1.9 + - - -
204G SER* 3.8 31.5 + - - -
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Residues in contact with GLN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C VAL* 3.8 24.4 - - + +
104G TRP* 2.9 24.9 + - + +
105G THR* 3.6 7.9 - - - +
107G SER* 1.3 75.9 - - - +
109G LYS* 1.3 57.3 + - - +
111G CYS* 3.3 2.0 + - - +
112G SER* 2.9 37.4 + - - -
116G ALA 4.3 2.0 + - - -
117G ASP* 2.8 29.5 + - - +
118G LEU* 2.8 43.6 + - + +
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Residues in contact with LYS 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G THR* 3.0 16.8 + - + +
106G LYS* 3.3 40.6 - - + +
107G SER 3.3 0.2 - - - -
108G GLN* 1.3 76.4 - - - +
110G ASN* 1.3 69.3 + - - +
112G SER* 3.2 7.2 + - - -
113G VAL* 3.0 39.1 + - + +
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Residues in contact with ASN 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G SER* 5.2 9.5 + - - +
102G GLN* 4.2 18.7 - - - +
106G LYS* 2.8 23.6 + - - +
107G SER* 3.2 11.7 + - - +
109G LYS* 1.3 82.1 - - - +
111G CYS* 1.3 62.2 + - - +
113G VAL* 3.3 23.0 - - - +
114G MET* 3.5 17.2 + - + +
206G CYS* 5.8 0.7 - - - -
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Residues in contact with CYS 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G SER 2.9 17.6 + - - -
108G GLN 3.6 7.0 - - - +
110G ASN* 1.3 75.2 - - - +
112G SER* 1.3 57.0 + - - +
114G MET* 3.0 20.7 + - - +
115G GLY 3.3 0.3 + - - -
116G ALA* 3.0 22.2 + - - +
117G ASP 3.7 17.5 - - - -
118G LEU* 3.7 24.5 - - - +
204G SER* 5.1 1.6 - - - -
206G CYS* 2.0 56.8 - - + -
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Residues in contact with SER 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G GLN* 2.9 27.3 + - - -
109G LYS* 3.2 9.7 + - - +
111G CYS* 1.3 78.4 - - - +
113G VAL* 1.3 62.5 + - - +
115G GLY* 3.1 13.2 + - - -
116G ALA 3.3 13.5 - - - -
117G ASP* 5.4 0.4 - - - -
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Residues in contact with VAL 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G LYS* 3.0 26.1 + - + +
110G ASN* 3.3 17.3 - - - +
112G SER* 1.3 77.1 - - - +
114G MET* 1.3 68.5 + - + +
115G GLY 3.1 1.1 + - - -
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Residues in contact with MET 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G TRP* 3.8 27.3 - - + +
96G PHE* 3.8 40.2 - - + -
98G SER* 6.0 0.4 - - - -
110G ASN* 3.5 23.6 - - + +
111G CYS* 3.0 7.4 + - - +
113G VAL* 1.3 83.7 - - + +
115G GLY* 1.3 59.6 + - - +
116G ALA* 4.7 0.2 - - - -
206G CYS* 3.9 17.9 - - - -
208G MET* 3.8 15.6 - - - +
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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