Contacts of the helix formed by residues 108 - 118 (chain I) in PDB entry 5BRR
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 GLY 108 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I VAL 3.4 1.0 + - - -
107I GLN* 1.3 74.3 - - - +
109I PHE* 1.3 59.9 + - - +
111I PRO* 3.7 18.2 - - - +
112I HIS* 3.4 21.0 + - - +
115I ARG* 5.4 1.6 + - - -
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Residues in contact with PHE 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 3.6 27.8 - - + -
49I THR* 3.7 20.9 - - + -
105I LEU* 5.5 3.1 - - + -
106I VAL* 3.7 18.5 + - + +
107I GLN 3.4 0.2 - - - -
108I GLY* 1.3 77.9 - - - +
110I MET* 1.3 101.1 + - + +
111I PRO* 3.0 2.0 - - - -
112I HIS* 2.8 11.1 + + - +
113I PHE* 2.7 38.9 + + + +
121I VAL* 4.6 2.0 - - + -
308I SER* 2.8 36.6 - - - +
309I LEU* 3.2 34.1 - - + -
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Residues in contact with MET 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I VAL* 5.7 0.2 - - + -
105I LEU* 3.8 31.9 - - + -
106I VAL 4.6 3.8 + - - +
109I PHE* 1.3 91.2 - - + +
111I PRO* 1.3 68.5 - - + +
113I PHE* 3.9 5.1 - - - +
114I PHE* 3.4 18.7 + - - +
120I THR* 4.5 9.5 + - - +
121I VAL* 3.2 56.3 - - + +
123I GLN* 4.4 9.2 - - + +
309I LEU* 4.8 3.8 - - + -
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Residues in contact with PRO 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I VAL 5.6 0.2 - - - +
108I GLY* 3.7 13.5 - - - +
109I PHE 3.2 11.7 - - - +
110I MET* 1.3 95.2 - - + +
112I HIS* 1.3 64.4 + - - +
113I PHE 3.1 1.3 - - - -
114I PHE* 3.1 10.3 + - + +
115I ARG* 2.9 38.4 + - - +
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Residues in contact with HIS 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.1 18.0 - - + +
67I ASP* 4.0 15.3 + - - -
108I GLY 3.4 19.4 + - - +
109I PHE* 2.8 13.7 + + - +
111I PRO* 1.3 75.2 - - - +
113I PHE* 1.3 57.7 + - - +
115I ARG* 3.0 40.1 + - - +
116I LEU* 3.1 46.2 + - + +
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Residues in contact with PHE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I MET* 4.3 26.7 - - + -
48I LEU* 3.6 29.6 - - + +
49I THR* 4.2 24.0 - - + -
97I ILE* 5.3 1.1 - - + -
109I PHE* 2.7 24.9 + + + +
110I MET* 3.9 10.3 - - - +
112I HIS* 1.3 70.7 - - - +
114I PHE* 1.3 65.8 + - - +
116I LEU 3.4 0.7 + - - +
117I PHE* 3.1 50.4 + + + +
119I SER* 3.5 22.4 - - - -
120I THR* 3.6 22.0 - - - -
121I VAL* 3.7 21.1 - - + -
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Residues in contact with PHE 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I MET 3.4 12.2 + - - +
111I PRO* 3.1 12.4 + - + +
113I PHE* 1.3 79.9 - - + +
115I ARG* 1.3 65.2 + - + +
118I ARG* 2.5 94.4 + - + +
119I SER 3.4 15.0 - - - +
120I THR* 5.4 3.6 - - - -
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Residues in contact with ARG 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ARG* 3.7 13.9 + - - -
108I GLY 5.4 1.2 + - - -
111I PRO* 2.9 27.1 + - - +
112I HIS* 3.0 39.0 + - - +
114I PHE* 1.3 85.1 - - - +
116I LEU* 1.3 62.5 + - + +
118I ARG* 4.3 6.9 - - - +
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LEU* 3.2 35.9 - - + -
66I ILE* 4.2 18.2 - - + +
67I ASP* 4.5 6.1 - - - +
72I ALA* 3.8 28.6 - - + +
73I PRO* 5.5 0.9 - - + -
76I ARG* 3.0 31.3 + - - +
112I HIS* 3.1 36.3 + - + +
113I PHE 4.0 3.8 - - - +
114I PHE 3.3 0.2 - - - -
115I ARG* 1.3 79.6 - - + +
117I PHE* 1.3 70.4 + - + +
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Residues in contact with PHE 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I SER 5.5 0.2 - - - -
44I ALA 3.7 3.1 - - - -
45I MET* 3.5 49.4 - - + -
48I LEU* 4.1 12.6 - - + -
66I ILE* 3.6 40.4 - - + -
72I ALA* 5.3 1.6 - - + -
75I LEU* 5.0 9.9 - - + -
76I ARG* 4.7 8.7 - - + +
113I PHE* 3.1 47.5 + + + +
116I LEU* 1.3 86.9 - - + +
118I ARG* 1.3 68.7 + - - +
119I SER* 2.8 18.6 + - - +
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Residues in contact with ARG 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ARG* 4.8 20.9 - - + +
80I LYS* 4.9 14.2 - - - +
114I PHE* 2.5 76.2 + - + +
115I ARG* 4.3 8.7 - - - +
117I PHE* 1.3 74.7 - - - +
119I SER* 1.3 59.3 + - - +
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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