Contacts of the helix formed by residues 40 - 54 (chain B) in PDB entry 2IHB
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 ASP 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B SER* 4.9 8.3 - - - -
30B TRP* 3.6 30.0 + - + +
36B ASN 3.3 11.1 + - - +
37B LEU 3.0 6.0 + - - +
39B GLU* 1.3 77.4 - - - +
41B PRO* 1.3 69.6 - - - +
42B GLU* 2.7 38.1 + - - +
43B GLY 2.8 5.5 + - - -
44B VAL* 2.9 21.0 + - - +
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Residues in contact with PRO 41 (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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38B LEU 5.7 0.2 - - - +
39B GLU 3.3 10.5 - - - +
40B ASP* 1.3 86.9 - - - +
42B GLU* 1.3 57.7 + - - +
44B VAL* 3.3 11.0 + - + +
45B LYS* 3.0 25.5 + - - +
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Residues in contact with GLU 42 (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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30B TRP* 3.9 16.4 - - + -
40B ASP* 2.7 18.5 + - - +
41B PRO* 1.3 72.5 - - - +
43B GLY* 1.3 62.6 + - - -
45B LYS* 3.2 23.0 + - - +
46B ARG* 3.1 55.5 + - - +
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Residues in contact with GLY 43 (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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30B TRP* 3.4 29.2 - - - -
37B LEU* 3.5 19.5 - - - +
40B ASP* 2.8 15.2 + - - -
42B GLU* 1.3 76.7 - - - +
44B VAL* 1.3 60.3 + - - +
46B ARG* 3.3 3.5 + - - +
47B PHE* 3.0 24.6 + - - +
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Residues in contact with VAL 44 (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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37B LEU* 3.6 1.1 + - - +
38B LEU* 3.5 45.5 - - + +
40B ASP 2.9 14.7 + - - +
41B PRO* 3.5 12.8 - - + +
42B GLU 3.3 0.2 - - - -
43B GLY* 1.3 75.8 - - - +
45B LYS* 1.3 57.1 + - - +
47B PHE* 3.7 7.0 - - - +
48B ARG* 2.8 42.1 + - + +
60B VAL* 4.6 4.3 - - + -
64B LEU* 3.8 33.9 - - + -
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Residues in contact with LYS 45 (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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41B PRO 3.0 12.7 + - - +
42B GLU* 3.5 27.7 + - - +
44B VAL* 1.3 79.6 - - - +
46B ARG* 1.3 84.3 + - - +
48B ARG* 3.4 10.2 + - - +
49B GLU* 3.1 38.5 + - + +
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Residues in contact with ARG 46 (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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30B TRP* 4.2 19.1 - - + -
42B GLU* 3.1 37.2 + - - +
43B GLY 3.9 4.0 - - - +
45B LYS* 1.3 97.9 - - - +
47B PHE* 1.3 61.9 + - - +
49B GLU* 3.4 33.4 + - - -
50B PHE 3.2 15.6 + - - -
138B PHE* 3.6 15.7 - - + -
143B LEU* 3.5 34.3 + - + +
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Residues in contact with PHE 47 (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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34B LEU* 4.1 16.4 - - + -
37B LEU* 3.7 16.8 - - + -
38B LEU* 4.3 15.3 - - + -
43B GLY 3.0 17.6 + - - +
44B VAL* 3.7 3.8 - - - +
46B ARG* 1.3 74.9 - - - +
48B ARG* 1.3 66.2 + - - +
50B PHE* 3.1 4.8 + + + +
51B LEU* 2.9 63.4 + - + +
60B VAL* 4.5 5.4 - - + -
130B MET* 4.1 24.2 - - + -
134B SER 4.5 0.7 - - - -
135B TYR* 4.1 31.9 - - + -
138B PHE* 3.7 32.7 - + + -
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Residues in contact with ARG 48 (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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44B VAL* 2.8 40.0 + - + +
45B LYS* 3.4 9.1 - - - +
47B PHE* 1.3 72.9 - - - +
49B GLU* 1.3 57.5 + - + +
51B LEU* 3.2 7.7 + - - +
52B LYS* 2.9 43.9 + - - +
57B GLU* 3.0 28.5 + - - +
60B VAL* 3.9 20.0 - - + -
61B LEU* 3.6 30.6 - - - +
64B LEU* 5.2 4.4 - - - +
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Residues in contact with GLU 49 (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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45B LYS* 3.1 33.4 + - + +
46B ARG* 3.6 40.0 + - - +
47B PHE 3.2 0.4 - - - -
48B ARG* 1.3 77.6 - - + +
50B PHE* 1.3 62.3 + - - +
52B LYS* 3.6 22.9 + - + +
53B LYS* 3.6 16.3 + - - +
143B LEU* 4.0 12.2 - - + +
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Residues in contact with PHE 50 (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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46B ARG 3.2 4.8 + - - +
47B PHE* 3.1 9.5 + + - +
49B GLU* 1.3 74.3 - - - +
51B LEU* 1.3 75.2 + - + +
53B LYS* 3.2 19.2 + - + +
54B GLU* 3.4 46.0 + - + +
134B SER* 3.4 22.2 - - - -
137B ARG* 3.7 8.3 - - + -
138B PHE* 3.4 49.4 - + + -
141B SER* 3.7 23.8 - - - -
143B LEU* 3.6 18.3 - - + +
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Residues in contact with LEU 51 (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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47B PHE* 2.9 44.6 + - + +
48B ARG* 3.7 4.9 - - - +
50B PHE* 1.3 76.6 - - + +
52B LYS* 1.3 67.6 + - - +
54B GLU* 3.0 4.3 + - - +
55B PHE 2.9 19.9 + - - -
56B SER* 3.1 36.6 + - - +
57B GLU* 3.7 16.2 - - - +
59B ASN* 5.1 0.7 - - + +
60B VAL* 3.5 40.6 - - + +
130B MET* 4.8 3.8 - - + -
134B SER* 3.7 26.9 - - - +
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Residues in contact with LYS 52 (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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48B ARG* 2.9 29.6 + - - +
49B GLU* 3.6 19.1 - - + +
51B LEU* 1.3 77.1 - - - +
53B LYS* 1.3 62.4 + - + +
55B PHE* 3.2 21.7 + - - +
57B GLU* 3.0 48.3 + - - +
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Residues in contact with LYS 53 (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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184A ILE 4.6 1.6 - - - +
49B GLU 3.6 11.1 + - - +
50B PHE* 3.2 14.5 + - + +
51B LEU 3.2 0.6 - - - -
52B LYS* 1.3 79.7 - - + +
54B GLU* 1.3 61.5 + - + +
55B PHE* 3.6 17.9 - - - -
143B LEU* 5.7 7.9 - - + -
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Residues in contact with GLU 54 (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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182A THR 4.8 1.6 - - - +
183A GLY* 3.1 5.2 - - - -
184A ILE 2.9 40.9 + - - +
185A VAL* 4.2 9.6 - - - +
50B PHE* 3.4 40.0 + - + +
51B LEU* 3.0 6.4 + - - +
53B LYS* 1.3 81.5 - - + +
55B PHE* 1.3 71.2 + - - +
56B SER* 3.3 8.4 + - - +
134B SER* 3.9 8.1 - - - -
137B ARG* 2.6 43.2 + - - -
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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