Contacts of the helix formed by residues 103 - 114 (chain C) in PDB entry 6UML
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 HIS 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C GLN* 3.6 35.6 + - - -
102C PHE* 1.3 81.2 - + + +
104C PRO* 1.3 69.5 - - + +
105C GLN* 4.2 14.8 - - + +
106C GLU* 3.0 25.5 + - + +
107C VAL* 2.9 25.5 + - - +
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Residues in contact with PRO 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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102C PHE 3.5 6.3 - - - +
103C HIS* 1.3 86.5 - - + +
105C GLN* 1.3 59.7 + - + +
107C VAL* 3.9 11.4 - - + -
108C SER* 2.7 36.6 + - - -
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Residues in contact with GLN 105 (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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85C PRO* 5.8 4.7 - - + -
103C HIS* 4.4 13.2 - - + -
104C PRO* 1.3 83.9 - - + +
106C GLU* 1.3 66.2 + - + +
108C SER* 3.3 5.3 + - - -
109C MET* 3.0 21.9 + - - +
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Residues in contact with GLU 106 (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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84C LEU* 5.5 3.6 - - + -
85C PRO* 3.4 40.8 - - + +
86C GLN* 3.3 22.3 - - - +
101C LEU* 3.6 29.9 - - + +
102C PHE 3.5 10.7 + - - -
103C HIS* 3.0 36.2 + - + +
105C GLN* 1.3 79.0 - - + +
107C VAL* 1.3 59.4 + - - +
109C MET* 2.8 28.6 + - - +
110C VAL* 3.0 18.1 + - + +
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Residues in contact with VAL 107 (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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101C LEU* 4.1 22.4 - - + +
102C PHE* 4.3 5.8 - - - +
103C HIS 2.9 21.9 + - - +
104C PRO* 3.8 9.0 - - + +
106C GLU* 1.3 74.5 - - - +
108C SER* 1.3 60.2 + - - +
110C VAL* 4.4 2.7 - - - +
111C ARG* 3.3 24.4 + - + +
146C GLU* 4.8 8.3 - - - +
153C GLU* 5.0 11.4 - - + +
155C VAL* 3.6 37.7 - - + +
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Residues in contact with SER 108 (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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104C PRO 2.7 21.8 + - - -
105C GLN* 3.5 5.6 - - - -
107C VAL* 1.3 71.9 - - - +
109C MET* 1.3 66.1 + - - +
110C VAL 3.1 0.3 + - - -
111C ARG* 3.2 4.5 + - - +
112C ASN* 3.0 37.7 + - - +
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Residues in contact with MET 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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82C PRO* 3.6 27.4 - - + -
83C VAL 4.5 10.1 - - - +
84C LEU* 3.5 30.5 - - + -
85C PRO* 5.2 6.7 - - + -
105C GLN 3.0 13.4 + - - +
106C GLU* 2.8 17.4 + - - +
108C SER* 1.3 72.1 - - - +
110C VAL* 1.3 56.9 + - + +
112C ASN* 4.1 2.7 - - - +
113C LEU* 2.8 45.5 + - + +
179C GLN* 6.2 2.9 - - + +
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Residues in contact with VAL 110 (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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84C LEU* 5.1 9.6 - - + -
101C LEU* 3.6 26.5 - - + -
106C GLU 3.0 15.1 + - - +
107C VAL 4.4 2.0 - - - +
109C MET* 1.3 79.5 - - + +
111C ARG* 1.3 66.9 + - - +
112C ASN 3.1 1.6 - - - -
113C LEU* 2.8 18.1 + - + +
114C ILE* 2.9 20.6 + - + +
141C ILE* 3.9 19.7 - - + -
144C TYR* 4.5 8.1 - - + -
155C VAL* 4.3 11.4 - - + -
157C VAL* 3.7 28.0 - - + -
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Residues in contact with ARG 111 (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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107C VAL* 3.3 20.4 + - + +
108C SER* 3.2 6.2 + - - +
110C VAL* 1.3 79.3 - - - +
112C ASN* 1.3 59.4 + - - +
114C ILE* 3.5 12.3 - - - +
115C GLN* 2.9 21.0 + - - +
144C TYR* 5.1 13.6 - - - +
146C GLU* 5.3 6.3 - - - +
155C VAL* 5.8 0.4 - - - +
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Residues in contact with ASN 112 (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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108C SER* 3.0 27.6 + - - +
109C MET* 4.3 2.5 - - - +
111C ARG* 1.3 75.6 - - - +
113C LEU* 1.3 60.2 + - - +
114C ILE 3.1 0.2 - - - -
115C GLN* 2.5 43.4 + - - +
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Residues in contact with LEU 113 (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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82C PRO* 3.8 29.2 - - + -
84C LEU* 5.4 0.9 - - + -
109C MET* 2.8 40.5 + - + +
110C VAL* 2.8 16.1 + - + +
112C ASN* 1.3 73.8 - - - +
114C ILE* 1.3 59.1 + - - +
115C GLN 2.6 19.2 - - - +
117C ASP* 5.7 3.8 - - + +
118C ARG* 3.0 25.7 + - - +
119C THR 4.4 15.9 - - - +
120C PHE* 4.3 20.2 - - + -
141C ILE* 5.0 6.1 - - + -
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Residues in contact with ILE 114 (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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67C PHE* 6.0 3.6 - - + -
110C VAL* 2.9 21.0 + - + +
111C ARG* 3.5 11.9 - - - +
113C LEU* 1.3 76.2 - - - +
115C GLN* 1.3 72.5 + - - +
116C LYS 3.4 1.7 + - - +
118C ARG* 3.2 33.6 - - + +
141C ILE* 5.3 10.5 - - + -
144C TYR* 4.2 39.9 - - + -
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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