Contacts of the helix formed by residues 116 - 127 (chain B) in PDB entry 2IAG
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B TYR* 1.3 80.0 - - - +
117B PRO* 1.3 69.2 - - - +
118B SER* 3.0 21.8 + - - -
119B ASP* 3.2 30.6 + - - +
120B GLU* 3.1 17.8 + - - +
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Residues in contact with PRO 117 (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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91B ARG* 3.6 28.9 - - - +
96B PHE* 4.1 20.2 - - + -
97B HIS* 3.4 40.6 - - + +
115B TYR* 3.2 18.5 - - + +
116B SER* 1.3 86.4 - - - +
118B SER* 1.3 59.0 + - - +
120B GLU* 4.0 1.7 - - - +
121B LYS* 3.0 33.9 + - - +
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Residues in contact with SER 118 (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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315A SER 5.6 0.4 - - - -
318A TRP* 3.4 40.2 + - - +
319A GLN 4.2 11.5 - - - -
91B ARG* 6.3 1.8 - - - -
96B PHE* 5.6 4.9 - - - -
116B SER* 3.0 11.3 + - - -
117B PRO* 1.3 80.1 - - - +
119B ASP* 1.3 65.3 + - - -
120B GLU 3.3 0.2 - - - -
121B LYS* 3.2 7.1 + - - +
122B ALA* 2.8 30.0 + - - +
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Residues in contact with ASP 119 (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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315A SER* 3.7 29.4 + - - +
319A GLN 5.5 1.7 - - - +
116B SER* 3.2 28.3 + - - +
118B SER* 1.3 83.1 + - - +
120B GLU* 1.3 57.1 + - - +
122B ALA* 3.4 8.1 + - - +
123B ARG* 2.9 29.0 + - - +
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Residues in contact with GLU 120 (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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115B TYR* 3.9 21.3 - - + -
116B SER 3.1 15.4 + - - +
117B PRO 4.0 3.1 - - - +
119B ASP* 1.3 75.4 - - - +
121B LYS* 1.3 61.3 + - + +
123B ARG* 2.8 45.7 + - - -
124B MET* 2.8 37.0 + - + +
259B TYR* 3.8 8.9 - - + -
262B HIS* 3.5 35.7 + - + +
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Residues in contact with LYS 121 (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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318A TRP* 3.6 35.4 - - + -
96B PHE* 5.0 9.1 - - + -
117B PRO 3.0 23.0 + - - +
118B SER* 3.2 5.4 + - - +
120B GLU* 1.3 77.2 - - + +
122B ALA* 1.3 57.7 + - - +
125B LYS* 2.9 34.4 + - - +
438B HIS 3.6 17.0 - - - +
439B ASN* 3.5 22.6 + - - +
442B LEU* 3.9 20.8 - - + +
600B HEM 3.4 40.2 + - + +
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Residues in contact with ALA 122 (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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311A GLY 5.2 0.4 - - - +
314A GLU* 3.8 6.2 - - + +
315A SER* 3.8 30.5 - - - +
318A TRP* 3.6 26.8 - - + +
118B SER 2.8 17.4 + - - +
119B ASP 3.5 5.4 - - - +
121B LYS* 1.3 77.7 - - - +
123B ARG* 1.3 60.8 + - - +
125B LYS* 3.7 2.1 - - - +
126B LEU* 3.5 29.1 + - - +
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Residues in contact with ARG 123 (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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119B ASP 2.9 19.9 + - - +
120B GLU* 2.8 43.3 + - - +
122B ALA* 1.3 71.8 - - - +
124B MET* 1.3 96.0 + - - +
125B LYS 3.4 0.3 + - - -
126B LEU* 3.4 12.1 + - - +
127B THR* 3.5 24.7 + - + +
255B TRP 4.6 1.4 + - - -
258B SER* 3.0 47.7 + - - -
259B TYR* 3.6 12.5 - - - +
262B HIS* 3.9 17.3 - - - +
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Residues in contact with MET 124 (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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120B GLU* 2.8 24.4 + - - +
123B ARG* 1.3 90.5 - - - +
125B LYS* 1.3 63.7 + - - +
127B THR* 2.7 24.0 + - - +
128B LEU* 3.6 10.6 - - + +
255B TRP* 3.5 32.5 - - + +
259B TYR* 3.5 39.0 - - + -
280B GLN* 4.1 17.9 - - - +
442B LEU* 4.0 9.0 - - + -
600B HEM 3.4 30.3 - - - -
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Residues in contact with LYS 125 (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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314A GLU* 4.7 17.9 - - - +
318A TRP* 4.7 8.1 - - - +
499A ARG* 4.6 11.9 - - - +
121B LYS 2.9 20.9 + - - +
122B ALA* 3.7 7.0 - - - +
123B ARG 3.2 0.2 - - - -
124B MET* 1.3 76.4 - - - +
126B LEU* 1.3 59.3 + - + +
128B LEU* 3.0 25.7 + - - +
129B LEU* 3.3 42.0 + - + +
440B HIS* 4.0 25.2 + - - -
441B CYS 4.3 7.3 + - - -
442B LEU* 4.0 37.7 + - + +
444B ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 126 (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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307A ALA 4.8 1.6 - - - +
310A ARG* 3.7 20.2 - - + +
311A GLY* 3.6 36.3 - - - +
314A GLU* 3.8 26.2 - - + +
122B ALA 3.5 16.8 + - - +
123B ARG* 3.4 7.2 + - - +
124B MET 3.3 0.6 - - - -
125B LYS* 1.3 71.8 - - + +
127B THR* 1.3 58.8 + - + +
128B LEU 3.0 9.1 + - - -
129B LEU* 3.4 24.1 + - + +
130B HIS* 4.0 28.1 + - + +
132B GLU* 4.2 7.0 - - - +
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Residues in contact with THR 127 (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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123B ARG* 3.5 21.0 + - + +
124B MET* 2.7 18.6 + - - +
126B LEU* 1.3 75.7 - - + +
128B LEU* 1.3 62.3 + - - +
129B LEU 3.6 0.4 - - - -
132B GLU* 3.6 23.6 - - - +
136B LEU* 4.1 8.0 - - - +
254B LYS* 4.0 13.0 - - + +
255B TRP* 3.6 38.7 + - - +
258B SER* 3.2 28.5 - - - +
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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