Contacts of the helix formed by residues 111 - 118 (chain A) in PDB entry 1IEQ
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 HIS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.4 8.4 + - + +
98A HIS* 3.1 36.0 + + + +
109A PHE 3.6 1.0 + - - -
110A PRO* 1.3 76.8 - - - +
112A ASN* 1.3 69.2 + - - +
113A VAL* 3.4 3.6 - - + +
114A GLY* 3.1 13.1 + - - -
115A LEU 3.3 6.6 + - - -
160A TYR* 3.5 36.1 - + + +
161A GLU* 5.1 3.0 - - + +
427A CYS 3.3 18.6 + - - -
429A GLY 2.7 29.5 + - - -
430A TRP* 4.2 7.4 - + + -
545A LEU* 3.2 38.9 + - + -
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Residues in contact with ASN 112 (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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97A VAL* 4.2 17.7 + - - +
110A PRO 5.1 0.2 - - - +
111A HIS* 1.3 75.1 + - - +
113A VAL* 1.3 64.3 + - - +
115A LEU* 2.9 24.7 + - - +
116A GLY 3.0 10.0 + - - -
146A PRO* 5.1 1.2 - - - +
147A CYS* 3.6 18.4 + - - +
160A TYR 3.4 1.4 + - - -
161A GLU* 3.0 37.5 + - - +
162A SER 4.0 1.3 - - - -
163A TYR* 3.3 48.9 + - + +
176A LEU* 5.8 1.2 - - - +
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Residues in contact with VAL 113 (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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111A HIS* 4.6 6.1 - - + +
112A ASN* 1.3 72.5 - - - +
114A GLY* 1.3 65.1 + - - +
116A GLY* 3.4 3.1 + - - -
159A CYS 4.8 0.7 - - - +
160A TYR* 3.0 29.6 + - + +
162A SER 3.4 18.3 + - - +
163A TYR 4.2 2.5 - - - +
525A GLY* 3.9 21.5 - - - +
544A TRP* 3.9 41.0 - - + -
545A LEU 5.2 0.7 - - - +
568A PRO* 3.3 25.4 - - + +
569A ARG* 4.3 24.0 - - + -
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Residues in contact with GLY 114 (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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110A PRO* 5.2 3.4 - - - -
111A HIS 3.1 6.7 + - - -
113A VAL* 1.3 85.5 - - - +
115A LEU* 1.3 62.6 + - - +
117A ALA* 3.1 12.3 + - - +
118A THR* 3.5 2.3 - - - +
388A SER* 3.0 26.1 - - - -
544A TRP* 3.5 30.9 - - - +
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Residues in contact with LEU 115 (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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109A PHE* 5.7 0.4 - - + -
110A PRO* 3.6 38.1 - - + +
111A HIS 3.3 3.0 + - - +
112A ASN* 2.9 26.5 + - - +
114A GLY* 1.3 78.5 - - - +
116A GLY* 1.3 58.1 + - - +
118A THR* 2.5 32.3 + - + -
119A ARG 3.9 1.0 + - - -
123A LEU* 5.1 1.3 - - + -
124A VAL* 4.2 20.6 - - + +
127A ILE* 3.6 38.4 - - + -
163A TYR* 4.2 10.8 - - + +
173A MET* 4.0 9.2 - - - +
176A LEU* 5.7 2.5 - - + -
384A ALA* 4.2 11.4 - - + +
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Residues in contact with GLY 116 (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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112A ASN 3.0 9.9 + - - -
113A VAL 3.4 0.6 + - - -
114A GLY 3.2 0.2 - - - -
115A LEU* 1.3 73.8 - - - +
117A ALA* 1.3 60.0 + - - +
118A THR 3.0 4.9 - - - -
119A ARG* 3.1 30.1 + - - -
163A TYR* 3.6 25.7 - - - -
169A ILE* 4.3 13.7 - - - +
173A MET* 4.7 4.0 - - - -
568A PRO* 3.8 6.7 - - - -
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Residues in contact with ALA 117 (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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113A VAL 4.1 0.4 - - - +
114A GLY 3.1 12.9 + - - +
116A GLY* 1.3 78.2 - - - +
118A THR* 1.3 57.8 + - - +
119A ARG* 3.9 4.0 + - - +
387A LYS 4.3 1.1 - - - -
388A SER 3.5 19.7 - - - +
390A VAL* 4.0 4.7 - - + -
544A TRP* 3.8 10.3 - - - +
564A THR 4.8 0.3 - - - +
565A GLY* 3.4 4.9 - - - -
566A ARG 3.0 43.4 + - - +
568A PRO* 3.2 18.2 - - + +
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Residues in contact with THR 118 (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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114A GLY 3.5 16.6 - - - +
115A LEU* 2.5 24.4 + - + +
117A ALA* 1.3 78.1 - - - +
119A ARG* 1.3 69.9 + - - +
120A ASP* 2.9 29.2 + - - +
123A LEU* 4.2 11.1 - - + +
124A VAL* 4.8 1.0 - - - +
384A ALA 4.1 4.0 - - - +
387A LYS* 3.5 41.5 - - + +
388A SER* 3.6 4.9 - - - +
564A THR 5.8 0.3 - - - +
565A GLY* 5.2 0.4 - - - -
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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