Contacts of the helix formed by residues 105 - 114 (chain C) in PDB entry 5DPR
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 PRO 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C ASP 3.4 15.7 - - - +
68C HIS* 4.0 25.8 - - + +
69C VAL 4.1 0.4 - - - +
103C SER 4.0 3.8 - - - +
104C THR* 1.3 95.5 - - + +
106C ILE* 1.3 58.2 + - - +
107C ALA* 3.0 6.3 - - + +
108C ASP* 2.9 41.5 + - - +
109C ILE* 3.3 7.8 + - - +
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Residues in contact with ILE 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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42C ILE* 3.8 16.2 - - + -
44C VAL* 3.7 30.1 - - + -
65C VAL* 3.9 18.2 - - + -
66C PRO 3.4 26.2 - - - +
67C ASP 3.4 2.8 + - - +
69C VAL 3.1 17.8 + - - +
70C ASN* 5.5 1.3 - - - +
71C MET* 5.0 8.3 - - - +
74C LEU* 4.7 4.3 - - + -
104C THR 3.5 1.2 + - - -
105C PRO* 1.3 71.0 - - - +
107C ALA* 1.3 59.6 + - - +
109C ILE* 3.2 14.3 + - + +
110C TYR* 2.8 28.4 + - - +
120C LEU* 3.9 17.3 - - + -
122C MET* 3.9 13.2 - - + -
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Residues in contact with ALA 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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42C ILE* 4.1 12.5 - - + +
67C ASP* 3.2 39.7 + - + +
68C HIS* 6.0 0.2 - - + -
105C PRO* 3.0 3.5 - - + -
106C ILE* 1.3 82.6 - - - +
108C ASP* 1.3 64.1 + - - +
110C TYR* 3.5 13.0 + - - +
111C GLU* 3.9 12.0 + - - +
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Residues in contact with ASP 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 THR* 3.7 13.9 - - + +
105C PRO* 2.9 33.4 + - - +
107C ALA* 1.3 79.8 - - - +
109C ILE* 1.3 66.2 + - - +
110C TYR 3.5 0.2 + - - -
111C GLU* 4.0 4.3 + - - +
112C GLN* 3.9 15.8 + - - +
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Residues in contact with ILE 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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71C MET* 5.0 4.7 - - + -
94C VAL* 4.1 7.9 - - + -
99C MET* 3.4 45.5 - - + -
101C SER* 4.4 12.6 - - - -
104C THR* 4.1 23.6 - - + +
105C PRO 3.7 11.4 - - - +
106C ILE* 3.2 17.2 + - + +
108C ASP* 1.3 77.8 - - - +
110C TYR* 1.3 59.5 + - - +
112C GLN* 3.2 4.2 + - - -
113C GLU* 2.8 38.1 + - + +
120C LEU* 4.5 8.5 - - + -
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Residues in contact with TYR 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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31C VAL* 4.1 4.5 - - - +
35C ARG* 3.4 44.7 - - - -
42C ILE* 3.4 41.5 - - + -
43C PRO* 4.0 7.6 - - + +
106C ILE 2.8 16.8 + - - +
107C ALA 3.6 8.3 - - - +
108C ASP 3.2 0.6 - - - -
109C ILE* 1.3 77.4 - - - +
111C GLU* 1.3 72.0 + - + +
114C LYS* 2.9 64.5 + - + +
118C GLY* 2.6 34.5 + - - -
120C LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 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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35C ARG* 3.8 11.8 + - - -
107C ALA 3.9 11.0 + - - +
108C ASP* 4.0 5.6 + - - +
109C ILE 3.4 0.4 - - - -
110C TYR* 1.3 89.8 - - + +
112C GLN* 1.3 61.1 + - - +
114C LYS* 3.1 41.6 + - - +
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Residues in contact with GLN 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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95C ASN* 5.3 0.7 + - - -
108C ASP 3.9 9.5 + - - +
109C ILE* 3.2 8.7 + - - +
111C GLU* 1.3 78.6 - - - +
113C GLU* 1.3 83.4 + - + +
114C LYS 3.7 0.6 - - - +
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Residues in contact with GLU 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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94C VAL* 4.1 5.2 - - + -
95C ASN* 3.1 42.1 + - + +
97C HIS* 3.0 32.3 + - - +
99C MET* 3.5 32.5 - - - +
109C ILE* 2.8 24.4 + - + +
112C GLN* 1.3 100.4 + - + +
114C LYS* 1.3 66.9 + - - +
115C ASP 3.8 0.7 + - - -
120C LEU* 3.8 12.8 - - + +
121C TYR 5.4 0.3 + - - -
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Residues in contact with LYS 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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35C ARG* 5.0 2.2 - - - +
95C ASN* 5.0 2.3 + - - +
110C TYR* 2.9 53.1 + - + +
111C GLU* 3.1 46.0 + - - +
112C GLN 3.7 1.7 - - - +
113C GLU* 1.3 81.6 - - - +
115C ASP* 1.3 67.4 + - - +
118C GLY* 4.2 8.7 - - - +
119C PHE 3.7 11.0 - - - +
120C LEU* 4.1 5.8 - - - -
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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