Contacts of the helix formed by residues 127 - 135 (chain D) in PDB entry 2IAM
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 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.4 17.9 - - - +
119C GLN 3.1 27.8 - - - -
120C LEU* 4.2 4.8 - - - +
125D GLU 3.8 0.4 + - - -
126D PRO* 1.3 74.6 - - - +
128D GLU* 1.3 61.7 - - - +
129D ALA* 3.1 11.7 + - - +
130D GLU* 2.5 49.0 + - - +
131D ILE* 3.1 16.6 + - - +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO 3.6 12.1 - - - +
127D SER* 1.3 69.0 - - - +
129D ALA* 1.3 67.4 + - - +
131D ILE* 3.2 15.9 + - + +
132D SER* 2.8 32.8 + - - +
197D TRP* 5.2 2.1 + - - -
238D ARG* 5.1 17.6 + - - -
240D ASP* 4.6 23.2 - - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.8 16.4 - - + -
119C GLN 6.0 0.2 - - - +
195C PHE* 4.6 10.0 - - + -
197C PRO* 4.3 17.9 - - + -
127D SER* 3.0 9.8 - - - +
128D GLU* 1.3 80.9 - - - +
130D GLU* 1.3 64.2 + - - +
132D SER* 3.8 5.0 - - - -
133D HIS* 3.2 23.4 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.5 35.8 - - + -
120C LEU* 5.4 1.0 - - - +
132C LEU* 4.1 7.1 - - - +
126D PRO* 3.8 7.1 - - - +
127D SER* 2.5 31.3 + - - +
129D ALA* 1.3 70.5 - - - +
131D ILE* 1.3 56.5 + - + +
133D HIS* 3.0 2.8 + - - +
134D THR* 2.7 45.4 + - - +
136D LYS 3.6 8.5 - - - +
137D ALA* 3.7 1.0 - - - -
138D THR* 2.5 52.2 + - - +
191D ARG* 2.9 23.5 + - - +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 4.8 2.9 - - + +
127D SER 3.1 15.4 + - - +
128D GLU* 3.5 19.7 - - + +
130D GLU* 1.3 74.3 - - - +
132D SER* 1.3 63.1 + - - +
135D GLN* 2.7 36.5 + - - +
136D LYS 3.4 17.0 - - - +
137D ALA* 3.9 12.3 - - + -
194D ALA* 3.6 12.3 - - + -
197D TRP* 3.7 33.4 - - + +
198D GLN* 3.6 27.6 - - + +
240D ASP 5.5 4.5 - - - +
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU* 2.8 23.9 + - - +
129D ALA* 3.8 5.4 - - - -
131D ILE* 1.3 76.4 - - - +
133D HIS* 1.3 58.0 + - - +
135D GLN* 3.9 14.1 + - - +
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Residues in contact with HIS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASP* 2.6 42.3 + - - +
118C TYR* 3.5 22.7 - - - +
195C PHE* 4.1 38.3 - + + +
129D ALA 3.2 15.8 + - - +
130D GLU 3.0 2.3 + - - +
131D ILE 2.9 0.8 + - - -
132D SER* 1.3 78.5 - - - +
134D THR* 1.3 63.4 + - + +
135D GLN* 3.5 3.6 - - - +
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Residues in contact with THR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASP* 4.3 14.6 - - + +
118C TYR* 4.6 2.7 - - - +
135C ASP* 3.5 25.4 - - - +
165C PHE* 6.0 0.9 - - + -
130D GLU* 2.7 31.2 + - - +
133D HIS* 1.3 79.0 - - + +
135D GLN* 1.3 70.1 + - - +
136D LYS* 3.0 42.7 + - + +
191D ARG* 3.8 6.8 + - - +
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 2.7 33.1 + - - +
132D SER* 3.9 13.1 + - - +
133D HIS 4.8 2.5 - - - +
134D THR* 1.3 76.3 - - - +
136D LYS* 1.3 59.1 + - + +
193D SER* 4.0 3.1 - - - -
194D ALA* 3.0 31.0 + - + +
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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