Contacts of the helix formed by residues 139 - 144 (chain A) in PDB entry 4MEI
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A TRP 3.3 20.7 + - - -
132A TYR* 2.8 24.9 + - - -
133A ALA 3.8 4.3 - - - -
136A ASN 2.9 16.2 + - - -
138A GLU* 1.3 78.1 - - - +
140A PRO* 1.3 76.1 - - - +
141A GLN* 3.2 14.7 + - - +
142A ASN* 2.9 19.4 + - - +
143A ILE* 3.0 12.6 + - - +
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Residues in contact with PRO 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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101A ARG 4.2 9.0 - - - +
102A GLU 5.8 1.8 - - - +
103A GLY 4.5 3.8 - - - +
104A PHE* 3.9 22.0 - - + -
131A TRP* 3.4 43.1 - - + -
132A TYR* 4.1 14.6 - - + -
138A GLU 3.8 0.2 - - - -
139A SER* 1.3 88.4 - - - +
141A GLN* 1.3 62.9 + - - +
143A ILE* 4.1 2.9 - - + -
144A TYR* 2.9 52.1 + - + +
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Residues in contact with GLN 141 (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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104A PHE* 3.6 21.3 - - + -
109A ALA* 5.6 4.2 - - + +
132A TYR* 3.0 52.7 + - + -
133A ALA* 4.5 0.2 - - - +
134A GLY* 3.3 22.8 - - - +
139A SER* 3.2 7.4 + - - +
140A PRO* 1.3 77.6 - - - +
142A ASN* 1.3 64.6 + - - +
144A TYR 4.0 0.3 - - - -
145A HIS* 3.3 31.7 - - - +
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Residues in contact with ASN 142 (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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134A GLY* 3.0 29.3 + - - +
135A ASN 4.4 0.6 - - - -
136A ASN 2.9 26.5 + - - -
137A PRO* 4.0 14.1 - - + +
139A SER* 2.9 11.3 + - - +
141A GLN* 1.3 81.9 - - - +
143A ILE* 1.3 61.1 + - - +
144A TYR 3.1 1.3 - - - -
145A HIS* 2.9 28.3 + - - +
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Residues in contact with ILE 143 (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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131A TRP* 6.0 2.0 - - + -
137A PRO 3.0 26.2 - - - +
138A GLU* 3.9 28.3 - - - +
139A SER 3.0 15.3 + - - +
140A PRO* 4.1 2.2 - - + -
142A ASN* 1.3 71.6 - - - +
144A TYR* 1.3 96.6 + - + +
145A HIS 3.5 0.6 - - - +
147A MET* 3.9 11.3 - - - +
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Residues in contact with TYR 144 (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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102A GLU 4.5 7.0 - - - -
104A PHE* 3.4 39.0 - - + -
140A PRO* 2.9 29.6 + - + +
141A GLN 4.0 0.4 - - - -
143A ILE* 1.3 109.2 - - + +
145A HIS* 1.3 63.7 + - - -
146A ASN 3.1 0.9 + - - -
147A MET* 3.1 25.4 + - + +
149A ALA* 3.9 17.9 - - + -
170A LYS* 3.1 35.4 + - + +
172A VAL* 3.6 33.8 - - + +
184A TRP* 5.5 2.3 - - - -
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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