Contacts of the helix formed by residues 138 - 143 (chain B) in PDB entry 1D2H
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 ASN 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY* 1.3 77.0 - - - +
139B SER* 1.3 63.9 + - - +
140B PHE 3.2 2.7 - - - -
141B ALA* 2.7 32.5 + - - +
142B HIS* 3.3 10.3 + - - +
173B ASP* 2.8 22.7 + - - -
174B HIS* 3.3 14.1 - - - +
175B LYS* 3.1 50.1 + - - +
177B TYR* 3.3 21.0 + - - -
242B TYR* 3.8 6.5 - - - -
283B TYR* 4.2 7.0 - - + -
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Residues in contact with SER 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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64B ALA* 3.1 26.3 - - - +
117B TRP* 3.6 11.7 - - - -
135B CYS* 3.9 13.4 + - - -
136B LEU 3.9 7.5 + - - -
137B GLY 2.8 4.1 + - - -
138B ASN* 1.3 76.0 - - - +
140B PHE* 1.3 60.4 + - - +
142B HIS* 2.8 35.3 + - - +
173B ASP* 4.1 2.6 + - - -
2301B SAH 2.7 34.1 + - - +
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TRP* 4.1 16.2 - + - -
135B CYS* 4.2 5.7 - - - -
138B ASN 3.2 1.0 - - - -
139B SER* 1.3 73.5 - - - +
141B ALA* 1.3 56.5 + - - +
142B HIS 2.9 10.2 + - - -
143B LEU* 3.2 18.5 + - + +
153B HIS* 3.7 23.1 - + + -
156B ALA* 3.7 19.1 - - + -
157B LEU* 2.6 50.0 - - + -
160B ILE* 4.1 10.1 - - + -
172B ILE* 4.3 13.0 - - + -
173B ASP 4.6 5.1 + - - +
174B HIS* 5.8 0.9 - - + -
245B HIS* 3.2 25.3 - + - +
250B PHE* 3.1 33.9 - + + -
253B LEU* 4.9 1.3 - - + -
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Residues in contact with ALA 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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138B ASN* 2.7 42.4 + - - +
140B PHE* 1.3 76.4 - - - +
142B HIS* 1.3 54.2 + - - +
143B LEU 3.4 0.7 - - - -
174B HIS* 5.2 1.3 - - + +
177B TYR* 4.1 4.0 - - + +
242B TYR* 2.6 42.1 - - + +
243B TYR* 2.7 27.6 + - - +
245B HIS* 4.6 10.7 + - - +
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Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TRP* 5.1 0.2 - - + -
137B GLY 4.7 1.4 + - - -
138B ASN* 3.3 17.6 + - - +
139B SER* 2.8 26.7 - - - +
140B PHE 2.9 0.8 - - - -
141B ALA* 1.3 81.1 - - - +
143B LEU* 1.3 52.3 + - - +
144B PRO* 2.6 26.4 - - - +
240B LEU* 4.4 24.1 - - + +
241B SER 4.7 5.7 - - - +
242B TYR* 4.2 26.9 - + - +
2301B SAH 3.8 61.2 + - + +
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Residues in contact with LEU 143 (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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117B TRP* 3.5 26.0 - - + -
118B LEU* 3.7 25.4 - - + -
139B SER 4.5 0.2 + - - -
140B PHE* 3.2 18.5 + - + +
141B ALA 5.0 1.1 - - - -
142B HIS* 1.3 76.2 - - - +
144B PRO* 1.3 76.0 - - + +
152B GLU* 4.3 13.9 - - + +
153B HIS* 3.1 33.7 + - + +
156B ALA* 3.4 32.3 - - + -
243B TYR* 4.1 9.6 - - - +
2301B SAH 4.6 7.6 - - - +
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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