Contacts of the helix formed by residues 103 - 109 (chain C) in PDB entry 2W93
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL 3.7 0.4 + - - -
102C PRO* 1.3 77.9 - - - +
104C ILE* 1.3 65.1 + - - +
105C SER* 3.3 7.8 + - - -
106C SER* 2.9 32.3 + - - -
107C GLN* 3.0 20.5 + - - +
168C PRO* 4.4 1.1 - - - -
169C ALA* 4.5 3.4 - - - +
170C ASN* 3.3 24.5 - - - +
559D THR 3.5 9.4 + - - -
560D ASN* 3.6 23.9 + - - -
562D LYS 4.0 4.7 - - - -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C SER* 1.3 70.8 - - - +
105C SER* 1.3 58.9 + - - +
107C GLN* 3.5 13.0 + - - +
108C ALA* 3.0 28.6 + - + +
139C ILE 4.0 0.9 - - - +
140C THR* 3.9 38.8 - - + +
168C PRO* 3.7 22.6 - - + +
170C ASN* 3.0 28.3 + - - +
171C LEU* 4.1 11.0 - - + -
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Residues in contact with SER 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C SER* 3.3 11.8 + - - -
104C ILE* 1.3 77.4 - - - +
106C SER* 1.3 63.4 + - - +
108C ALA* 3.3 6.1 + - - +
109C LYS* 2.9 52.8 + - - +
170C ASN* 5.5 0.6 - - - -
559D THR 5.0 0.3 + - - -
562D LYS* 3.6 23.3 + - - +
563D GLN 4.4 14.0 + - - -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.0 8.3 - - - -
103C SER* 2.9 28.2 + - - -
105C SER* 1.3 75.7 + - - +
107C GLN* 1.3 56.9 + - - +
109C LYS* 3.5 0.9 + - - -
110C GLN* 3.0 21.7 + - - -
111C LEU* 3.1 26.8 + - - +
113C LEU* 3.8 22.4 - - - +
122C PHE* 4.0 3.5 - - - -
559D THR* 3.4 28.4 + - - +
560D ASN* 5.1 1.0 + - - -
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Residues in contact with GLN 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 3.7 17.4 - - - +
102C PRO* 2.9 27.3 + - + +
103C SER 3.0 15.5 + - - +
104C ILE* 3.6 14.6 - - - +
106C SER* 1.3 74.1 - - - +
108C ALA* 1.3 58.2 + - - +
110C GLN* 2.8 29.8 + - - +
122C PHE* 3.9 47.9 - - + +
138C MET* 4.8 9.0 - - - +
168C PRO* 4.2 9.7 - - - +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 3.0 20.8 + - + +
105C SER* 3.3 7.8 + - - +
107C GLN* 1.3 75.9 - - - +
109C LYS* 1.3 62.9 + - + +
110C GLN* 3.4 10.2 + - - +
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C SER* 2.9 39.7 + - - +
106C SER 3.9 3.6 - - - +
108C ALA* 1.3 77.3 - - + +
110C GLN* 1.3 72.1 + - - +
111C LEU* 3.1 28.7 + - + +
562D LYS* 5.2 13.5 - - - +
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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