Contacts of the helix formed by residues 133 - 141 (chain B) in PDB entry 6U07
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 SER 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.4 23.0 - - - -
129A GLN 3.4 26.7 - - - -
130A LEU* 4.4 3.6 - - - +
207A PRO* 6.2 0.2 - - - -
131B GLU 3.6 1.6 + - - -
132B PRO* 1.3 73.9 - - - +
134B LYS* 1.3 63.6 + - - +
135B ALA* 3.4 6.8 + - - +
136B GLU* 3.0 31.7 + - - +
137B ILE* 3.2 15.4 + - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO 3.8 2.2 + - - -
133B SER* 1.3 71.4 - - - +
135B ALA* 1.3 61.7 + - - +
137B ILE* 3.2 6.1 + - - +
138B SER* 2.9 32.3 + - - -
246B ASP* 3.3 49.1 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.8 4.3 - - + -
205A PHE* 4.5 6.2 - - + -
207A PRO* 3.5 40.8 - - + -
133B SER* 3.1 8.0 + - - +
134B LYS* 1.3 79.6 - - - +
136B GLU* 1.3 57.2 + - - +
138B SER* 3.5 5.3 + - - -
139B ARG* 3.0 31.9 + - - +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A TYR* 3.4 38.8 - - + +
130A LEU* 5.7 1.2 - - - +
142A LEU* 4.7 4.5 - - - +
144A THR* 4.9 0.3 - - - +
132B PRO* 4.4 4.5 - - - +
133B SER* 3.0 22.3 + - - +
135B ALA* 1.3 73.6 - - - +
137B ILE* 1.3 59.6 + - - +
140B THR* 2.6 47.0 + - - +
142B LYS 3.5 7.4 - - - +
143B ALA* 3.7 1.7 - - - -
144B THR* 2.6 52.2 + - - +
197B ARG* 2.9 21.7 + - - +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 4.3 5.8 - - + +
133B SER 3.2 19.1 + - - +
134B LYS 3.2 5.1 + - - +
136B GLU* 1.3 75.3 - - - +
138B SER* 1.3 61.0 + - - +
141B GLN* 2.9 35.5 + - - +
142B LYS 3.4 16.6 - - - +
143B ALA* 4.0 12.3 - - + -
200B ALA* 3.8 19.3 - - + -
203B TRP* 3.7 31.2 - - + +
204B GLN* 4.0 12.6 - - + +
246B ASP* 3.5 33.4 - - + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 2.9 27.9 + - - -
135B ALA* 3.7 6.1 - - - -
137B ILE* 1.3 79.4 - - - +
139B ARG* 1.3 60.8 + - - +
141B GLN* 3.3 18.9 + - - +
246B ASP* 5.5 0.9 - - - -
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP* 2.8 41.2 + - - +
125A PRO 5.1 0.2 + - - -
126A ALA* 5.0 0.2 - - - +
128A TYR* 3.6 14.8 - - - +
203A ASP 4.9 6.3 + - - -
205A PHE* 3.5 59.9 - - + +
135B ALA 3.0 17.8 + - - +
138B SER* 1.3 79.0 - - - +
140B THR* 1.3 61.0 + - - +
141B GLN* 5.2 1.0 - - - +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP* 4.0 15.0 - - + +
128A TYR* 3.6 20.2 - - - +
145A ASP* 3.9 18.2 - - - +
136B GLU* 2.6 28.6 + - + +
139B ARG* 1.3 79.8 - - - +
141B GLN* 1.3 72.2 + - - +
142B LYS* 3.1 34.5 + - - +
197B ARG* 3.9 8.0 + - - +
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET* 5.5 1.0 - - - +
137B ILE* 2.9 19.3 + - - +
138B SER* 3.3 24.9 + - - +
139B ARG 5.2 0.9 - - - +
140B THR* 1.3 78.9 - - - +
142B LYS* 1.3 62.0 + - - +
199B SER* 3.9 4.5 - - - -
200B ALA* 3.0 31.6 + - + +
204B GLN* 5.8 0.2 + - - -
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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