Contacts of the helix formed by residues 152 - 161 (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 PRO 152 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ILE* 4.9 8.1 - - + -
134I HIS* 4.1 22.9 - - + +
150I ILE 3.5 2.6 - - - +
151I LEU* 1.3 85.1 - - + +
153I ALA* 1.3 64.7 + - - +
154I ASP* 4.6 1.8 - - + +
155I ARG* 4.2 35.0 - - + +
156I ILE* 3.2 25.1 + - - +
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Residues in contact with ALA 153 (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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93I SER 3.4 24.2 - - - +
94I VAL* 4.5 10.3 - - + -
95I GLY 5.5 2.0 - - - +
151I LEU 3.2 3.0 + - - +
152I PRO* 1.3 71.0 - - - +
154I ASP* 1.3 64.9 + - - +
156I ILE* 3.3 2.3 + - - +
157I THR* 2.9 37.1 + - + +
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Residues in contact with ASP 154 (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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152I PRO* 3.4 2.8 - - + +
153I ALA* 1.3 81.2 - - - +
155I ARG* 1.3 59.1 + - + +
157I THR* 2.5 23.8 + - - +
158I GLU* 2.9 15.1 + - - +
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Residues in contact with ARG 155 (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* 4.7 23.9 - - + +
133I GLU* 5.0 10.9 + - - -
152I PRO* 3.9 28.8 + - + +
153I ALA 3.4 0.4 - - - -
154I ASP* 1.3 78.3 - - + +
156I ILE* 1.3 64.2 + - + +
158I GLU* 2.9 12.6 + - + +
159I VAL* 2.9 21.0 + - - +
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Residues in contact with ILE 156 (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* 3.8 22.0 - - + +
93I SER* 3.3 26.5 - - - +
94I VAL* 3.6 19.5 - - + -
127I LEU* 3.8 20.6 - - + -
130I ILE* 4.5 19.5 - - + -
151I LEU* 3.6 19.1 - - + -
152I PRO 3.2 14.3 + - - +
153I ALA 3.3 5.0 + - - +
155I ARG* 1.3 76.0 - - + +
157I THR* 1.3 63.7 + - - +
159I VAL* 2.9 26.1 - - - +
160I LEU* 2.9 15.3 + - + +
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Residues in contact with THR 157 (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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94I VAL* 4.6 8.1 - - + -
95I GLY 5.7 0.7 - - - +
153I ALA* 2.9 20.4 + - + +
154I ASP* 2.5 29.8 + - - +
156I ILE* 1.3 76.3 - - - +
158I GLU* 1.3 56.4 + - - +
160I LEU* 3.3 10.6 + - - +
161I LYS* 3.0 33.2 + - - +
177I LEU* 3.8 33.0 - - + -
179I SER* 4.5 13.0 - - - +
180I THR* 4.0 3.3 - - - +
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Residues in contact with GLU 158 (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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154I ASP 2.9 12.9 + - - +
155I ARG* 2.9 16.3 + - + +
157I THR* 1.3 75.6 + - - +
159I VAL* 1.3 69.6 + - - +
161I LYS* 3.3 26.4 + - + +
162I SER* 3.8 4.3 + - - -
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Residues in contact with VAL 159 (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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123I ALA* 3.8 18.0 - - + +
126I GLU* 3.7 38.1 - - + +
127I LEU* 3.4 31.6 - - + +
130I ILE* 4.7 9.2 - - + -
155I ARG 2.9 10.3 + - - +
156I ILE* 2.9 25.5 + - - +
158I GLU* 1.3 82.4 + - - +
160I LEU* 1.3 61.9 + - + +
161I LYS 3.0 0.2 - - - -
162I SER* 2.9 30.3 + - - +
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Residues in contact with LEU 160 (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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94I VAL* 5.1 6.7 - - + -
117I PHE* 4.7 17.3 - - + -
119I LEU* 3.8 33.2 - - + +
123I ALA* 5.8 1.8 - - + -
127I LEU* 4.3 19.1 - - + -
156I ILE* 2.9 31.9 + - + +
157I THR* 3.3 6.9 + - - +
159I VAL* 1.3 79.4 - - + +
161I LYS* 1.3 57.9 + - - +
162I SER* 3.2 1.8 + - - +
172I ARG* 3.0 28.1 + - - +
174I LEU* 5.5 4.7 - - + -
177I LEU* 3.8 26.2 - - + -
180I THR* 3.8 13.0 - - + +
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Residues in contact with LYS 161 (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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157I THR* 3.0 20.8 + - - +
158I GLU* 3.5 18.2 - - + +
159I VAL 3.0 1.2 - - - -
160I LEU* 1.3 77.3 - - - +
162I SER* 1.3 65.9 + - - +
163I ARG* 3.4 33.7 + - - +
172I ARG* 4.5 2.0 + - - +
179I SER* 3.4 47.7 + - - +
180I THR* 4.0 13.6 - - + +
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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