Contacts of the helix formed by residues 132 - 140 (chain A) in PDB entry 5T4S
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 PHE 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 2.6 25.6 + - - -
131A GLY* 1.3 74.3 - - - -
133A ILE* 1.3 65.6 + - - +
134A GLU* 3.2 15.5 - - - +
135A GLN 3.2 6.2 + - - -
142A PRO* 3.9 1.1 - - - -
195A LEU* 3.8 20.9 - - + -
198A THR* 3.6 17.3 - - - -
199A GLY* 3.3 40.4 + - - +
200A VAL* 3.6 6.3 - - - -
201A TRP* 3.4 50.5 - + - -
329A ARG* 3.6 40.4 - - + +
332A ASN* 3.8 9.2 - - - -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 1.3 72.1 - - - +
134A GLU* 1.3 73.7 + - + +
136A ALA* 2.9 27.7 + - + +
139A ARG* 4.1 20.3 - - + +
140A VAL 4.1 7.0 - - - +
141A THR* 4.0 26.9 - - + +
142A PRO* 3.6 24.8 - - + +
145A ASP* 4.5 11.9 + - - +
329A ARG* 4.9 2.9 - - - +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 3.2 18.4 - - - +
133A ILE* 1.3 86.6 - - + +
135A GLN* 1.3 71.3 + - - +
136A ALA 3.7 2.3 + - - +
198A THR* 4.0 19.0 + - - +
199A GLY* 3.7 26.9 + - - +
329A ARG* 5.5 0.5 + - - -
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 5.7 3.1 - - - +
41A SER* 5.6 4.6 - - - -
42A SER* 3.6 22.2 + - - +
43A ASN* 4.5 1.0 - - - +
131A GLY* 5.9 0.4 - - - -
132A PHE 3.2 3.5 + - - +
133A ILE 3.2 0.6 - - - -
134A GLU* 1.3 87.3 + - - +
136A ALA* 1.3 61.3 + - - +
137A ILE* 3.5 13.8 + - - +
197A LYS* 5.5 1.2 - - - +
199A GLY* 3.3 18.2 + - - +
200A VAL* 3.4 30.6 - - + +
308A PRO* 5.9 6.3 - - - +
309A THR* 4.5 11.4 + - - -
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 3.7 19.7 - - - +
43A ASN* 3.6 8.5 - - - +
132A PHE 3.7 0.8 + - - -
133A ILE* 2.9 22.2 + - + +
134A GLU 4.6 2.6 - - - +
135A GLN* 1.3 76.6 - - - +
137A ILE* 1.3 64.8 + - - +
138A GLY 3.6 0.3 + - - -
139A ARG* 3.3 14.7 + - - +
140A VAL* 3.3 31.2 - - + +
142A PRO* 4.6 0.2 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.0 31.6 + - - +
79A LEU* 4.2 16.1 - - + +
80A THR 3.6 22.9 - - - +
81A LEU* 3.9 23.6 - - + -
82A ARG 5.7 1.1 - - - +
135A GLN 4.3 10.8 - - - +
136A ALA* 1.3 71.6 - - - +
138A GLY* 1.3 62.4 + - - +
140A VAL* 3.1 10.9 - - - +
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A THR* 6.6 0.2 - - - -
79A LEU* 5.9 2.2 - - - -
92A LEU* 5.2 11.4 - - - +
136A ALA 3.6 0.4 + - - -
137A ILE* 1.3 74.7 - - - +
139A ARG* 1.3 70.0 + - - +
140A VAL* 3.1 8.1 + - - +
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.1 18.4 - - + +
136A ALA* 3.3 14.5 + - - +
137A ILE 3.3 2.2 - - - -
138A GLY* 1.3 78.1 - - - +
140A VAL* 1.3 63.0 + - - +
141A THR* 3.6 2.9 + - - -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER 4.8 0.7 - - - +
43A ASN* 3.2 22.7 - - + +
92A LEU* 4.5 18.4 - - + -
106A GLN* 4.5 0.4 - - - +
107A MET* 3.4 46.2 - - + +
133A ILE* 4.1 1.2 - - - +
136A ALA* 3.3 21.3 - - + +
137A ILE 3.1 22.2 + - - +
138A GLY* 3.1 5.4 + - - +
139A ARG* 1.3 75.4 - - - +
141A THR* 1.3 76.3 + - - +
142A PRO* 3.2 5.4 - - - +
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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