Contacts of the helix formed by residues 121 - 134 (chain I) in PDB entry 5U07
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 VAL 121 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I LYS* 3.2 28.8 + - + +
60I VAL* 3.6 25.8 - - + -
72I ARG* 3.1 45.2 + - - +
120I PRO* 1.3 71.4 - - - +
122I PRO* 1.3 66.7 - - + +
124I ILE* 2.8 24.5 + - + +
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Residues in contact with PRO 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ASP* 4.9 7.0 - - - +
58I LYS 4.6 3.4 - - - +
120I PRO* 3.5 13.0 - - + -
121I VAL* 1.3 93.2 - - + +
123I ALA* 1.3 53.0 + - - +
125I ASP* 3.0 12.3 + - + +
126I GLU* 2.6 47.2 + - - +
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Residues in contact with ALA 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I LEU* 4.3 9.9 - - + -
120I PRO* 3.1 23.2 + - + +
121I VAL 3.1 0.8 - - - -
122I PRO* 1.3 76.8 - - - +
124I ILE* 1.3 65.2 + - - +
126I GLU* 3.0 12.4 + - - +
127I LEU* 2.9 28.1 + - + +
159I VAL* 3.8 14.8 - - + +
160I LEU* 5.8 1.8 - - + -
162I SER* 3.5 24.9 - - - +
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Residues in contact with ILE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I VAL* 4.8 17.3 - - + -
62I THR* 5.6 0.4 - - + -
65I ILE* 3.8 20.0 - - + -
68I GLU* 3.0 35.7 - - + +
69I ILE* 3.5 16.3 - - + +
72I ARG* 3.3 23.1 - - - +
119I LEU* 3.4 23.6 - - + -
120I PRO 3.3 0.9 + - - +
121I VAL* 2.8 18.6 + - - +
123I ALA* 1.3 77.9 - - - +
125I ASP* 1.3 61.6 + - - +
127I LEU* 3.1 10.7 + - - +
128I ALA* 2.9 20.8 + - - +
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Residues in contact with ASP 125 (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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72I ARG* 3.1 23.7 - - - +
76I ARG* 2.4 36.1 + - - -
121I VAL 3.1 0.2 + - - -
122I PRO* 3.0 17.3 + - + +
124I ILE* 1.3 76.4 - - - +
126I GLU* 1.3 62.7 + - - +
128I ALA* 3.2 5.2 + - - +
129I ALA* 3.0 18.6 + - - +
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Residues in contact with GLU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I PRO* 2.6 40.4 + - - +
123I ALA* 3.0 14.4 + - - +
125I ASP* 1.3 78.4 - - + +
127I LEU* 1.3 58.7 + - - +
129I ALA* 3.1 8.5 + - + +
130I ILE* 2.9 37.0 + - + +
159I VAL* 3.7 20.3 - - + +
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Residues in contact with LEU 127 (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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65I ILE* 4.8 13.5 - - + -
69I ILE* 4.5 19.3 - - + -
90I VAL* 3.9 22.9 - - + +
91I VAL* 6.5 0.4 - - + -
119I LEU* 5.2 3.4 - - + -
123I ALA 2.9 18.6 + - - +
124I ILE* 3.1 13.9 + - - +
126I GLU* 1.3 75.2 - - - +
128I ALA* 1.3 62.2 + - - +
130I ILE* 3.3 7.0 + - + +
131I ALA* 2.9 24.8 + - - +
156I ILE* 3.8 23.1 - - + -
159I VAL* 3.4 26.9 - - + +
160I LEU* 4.3 17.5 - - + -
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Residues in contact with ALA 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ILE* 4.9 7.3 - - + +
72I ARG* 4.3 16.6 - - + -
73I LEU* 3.3 28.4 - - + +
76I ARG* 3.3 23.6 - - - +
124I ILE 2.9 12.8 + - - +
125I ASP* 3.2 9.6 + - - +
127I LEU* 1.3 77.0 - - - +
129I ALA* 1.3 56.1 + - - +
131I ALA* 3.3 2.9 + - - +
132I ASP* 2.9 24.6 + - - +
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Residues in contact with ALA 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ARG* 3.7 14.5 - - - +
125I ASP* 3.0 13.3 + - - +
126I GLU* 3.1 11.4 + - + +
128I ALA* 1.3 77.3 - - - +
130I ILE* 1.3 59.6 + - + +
132I ASP* 2.9 22.5 + - - +
133I GLU* 3.0 16.2 + - - +
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Residues in contact with ILE 130 (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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90I VAL* 5.7 1.1 - - + -
126I GLU* 2.9 26.1 + - + +
127I LEU* 3.8 7.2 - - + +
129I ALA* 1.3 77.2 - - + +
131I ALA* 1.3 61.9 + - - +
132I ASP 3.3 0.3 + - - -
133I GLU* 3.6 9.6 + - - +
134I HIS* 3.3 26.9 - - + +
151I LEU* 3.4 16.3 - - + +
152I PRO* 4.9 9.6 - - + -
155I ARG* 4.7 35.9 - - + +
156I ILE* 4.5 23.6 - - + -
159I VAL* 4.7 13.2 - - + -
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Residues in contact with ALA 131 (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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73I LEU* 3.9 21.7 - - + +
78I TRP* 3.7 16.3 - - - -
86I GLY* 4.3 18.0 - - - +
90I VAL* 4.6 12.5 - - + +
127I LEU 2.9 17.1 + - - +
128I ALA* 3.7 4.9 - - - +
130I ILE* 1.3 76.7 - - - +
132I ASP* 1.3 60.7 + - - +
134I HIS* 4.0 8.4 + - - +
138I VAL* 4.4 7.6 - - + +
151I LEU* 4.1 12.1 - - + +
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Residues in contact with ASP 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I LEU* 4.5 2.5 - - + -
76I ARG* 4.2 19.8 + - - +
78I TRP* 3.0 34.3 + - - +
128I ALA 2.9 13.1 + - - +
129I ALA* 2.9 14.1 + - - +
131I ALA* 1.3 75.5 - - - +
133I GLU* 1.3 64.5 + - - +
134I HIS 3.1 4.0 + - - -
135I ARG* 3.4 25.6 + - - +
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Residues in contact with GLU 133 (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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129I ALA 3.0 14.2 + - - +
130I ILE* 3.6 9.6 + - - +
131I ALA 3.6 0.4 - - - -
132I ASP* 1.3 76.0 - - - +
134I HIS* 1.3 73.8 + - + +
135I ARG* 3.5 3.1 + - - -
155I ARG* 5.0 10.5 + - - -
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Residues in contact with HIS 134 (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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130I ILE* 3.3 17.4 + - + +
131I ALA 4.0 3.6 + - - +
132I ASP 3.1 2.1 - - - -
133I GLU* 1.3 94.3 + - + +
135I ARG* 1.3 61.9 + - - +
136I ASP 3.4 2.7 - - - -
137I ALA* 3.3 16.9 + - + +
138I VAL* 3.1 27.6 + - + +
150I ILE* 5.7 5.5 - - + +
151I LEU* 3.3 36.6 - - + -
152I PRO* 4.1 19.6 - - + +
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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