Contacts of the helix formed by residues 37 - 50 (chain B) in PDB entry 3HIG
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP 3.5 2.0 + - - -
36B LEU* 1.3 74.6 - - - +
38B ASN* 1.3 65.5 + - - +
39B GLN* 3.3 11.2 + - - +
40B GLU* 3.0 35.9 + - - +
41B LEU* 3.0 24.3 + - - +
401B PHE* 4.8 2.9 - - - -
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Residues in contact with ASN 38 (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 SER* 1.3 71.7 - - - +
39B GLN* 1.3 61.9 + - - +
41B LEU* 3.3 4.4 + - - +
42B LYS* 3.1 41.1 + - - +
401B PHE* 3.2 53.2 - - + -
409B PRO* 3.6 17.3 - - - +
751B VAL* 3.1 31.4 + - - +
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Residues in contact with GLN 39 (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 SER* 3.2 10.3 + - - +
38B ASN* 1.3 80.8 - - - +
40B GLU* 1.3 57.0 - - + +
42B LYS* 3.5 10.3 + - - +
43B ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 40 (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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35B ASP 3.9 0.2 - - - +
36B LEU* 3.3 16.5 - - + -
37B SER* 3.0 39.4 + - - +
39B GLN* 1.3 75.2 - - + +
41B LEU* 1.3 65.2 + - - +
43B ALA* 3.2 7.9 + - - +
44B VAL* 3.0 29.2 + - - +
95B ARG* 2.7 46.2 + - - -
119B LEU* 4.1 20.0 - - + +
120B PRO* 5.4 3.7 - - + -
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Residues in contact with LEU 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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36B LEU* 3.6 30.3 - - + +
37B SER 3.0 21.9 + - - +
38B ASN 3.8 1.1 - - - +
40B GLU* 1.3 74.8 - - - +
42B LYS* 1.3 57.4 + - - +
44B VAL* 3.3 5.2 + - - +
45B HIS* 3.0 30.1 + - - +
72B ILE* 3.5 41.1 - - + +
73B GLU* 5.0 0.4 - - - -
401B PHE* 3.9 34.3 - - + +
403B TYR* 3.9 13.0 - - + +
409B PRO* 3.6 27.1 - - + +
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Residues in contact with LYS 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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38B ASN* 3.1 37.6 + - - +
39B GLN* 3.6 7.6 - - - +
41B LEU* 1.3 75.6 - - - +
43B ALA* 1.3 54.4 + - - +
45B HIS* 3.6 6.3 - - - +
46B SER* 2.8 39.8 + - - +
408B ASP* 6.4 0.7 - - - -
409B PRO* 4.0 18.8 - - + +
751B VAL* 2.6 33.3 + - - -
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Residues in contact with ALA 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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39B GLN 3.0 17.4 + - - +
40B GLU* 3.5 9.4 - - - +
41B LEU 3.2 0.2 - - - -
42B LYS* 1.3 77.2 - - - +
44B VAL* 1.3 63.0 + - + +
46B SER* 4.0 4.8 - - - -
47B PHE* 3.1 23.6 + - - +
119B LEU* 5.4 2.9 - - + -
120B PRO* 6.4 0.7 - - + -
121B GLY 5.8 1.6 - - - +
122B PRO* 3.7 21.6 - - + +
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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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36B LEU* 4.7 0.9 - - + -
40B GLU 3.0 17.0 + - - +
41B LEU 3.8 3.8 - - - +
43B ALA* 1.3 76.2 - - - +
45B HIS* 1.3 62.0 + - - +
47B PHE* 3.4 6.1 + - - +
48B LEU* 3.1 33.5 + - + +
72B ILE* 3.8 30.1 - - + -
97B ALA* 3.7 22.0 - - + -
99B ALA* 4.8 1.3 - - + -
116B VAL* 4.0 25.1 - - + -
119B LEU* 4.0 23.6 - - + -
122B PRO* 4.6 2.7 - - - -
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Residues in contact with HIS 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 LEU 3.0 17.8 + - - +
42B LYS* 3.6 7.4 - - - +
44B VAL* 1.3 74.6 - - - +
46B SER* 1.3 67.0 + - - +
48B LEU* 3.4 4.5 + - - +
49B TRP* 3.0 68.5 + + - -
69B VAL* 4.6 7.2 - - + +
72B ILE* 4.1 11.2 - - + +
403B TYR* 3.0 41.0 + + + -
407B ASP 3.5 21.6 + - - -
408B ASP* 4.7 7.7 + - - -
409B PRO* 5.6 3.7 - - + +
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Residues in contact with SER 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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42B LYS* 2.8 22.5 + - - +
43B ALA* 4.0 5.6 - - - -
45B HIS* 1.3 73.4 + - - +
47B PHE* 1.3 63.9 + - - +
49B TRP* 3.2 7.0 + - - +
50B SER* 2.9 24.3 + - - -
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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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43B ALA 3.1 16.5 + - - +
44B VAL 3.5 2.9 - - - +
46B SER* 1.3 79.1 - - - +
48B LEU* 1.3 69.2 + - + +
50B SER* 2.7 28.5 + - - -
51B LYS* 3.5 41.8 + - - +
116B VAL* 3.7 21.5 - - + -
122B PRO* 3.7 22.9 - - + -
123B CYS* 3.7 35.4 - - - -
124B TYR 3.5 21.8 - - - -
125B MET* 4.2 5.4 - - + -
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Residues in contact with LEU 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* 3.1 31.7 + - + +
45B HIS* 3.9 4.3 - - - +
47B PHE* 1.3 83.7 - - + +
49B TRP* 1.3 58.7 + - - +
51B LYS* 3.1 26.0 + - - +
54B LEU* 3.7 6.6 - - + +
56B LEU* 3.6 22.4 - - + +
69B VAL* 3.9 24.7 - - + -
72B ILE* 4.9 0.9 - - + -
99B ALA* 3.9 26.0 - - + -
101B ILE* 4.6 3.8 - - + -
114B PHE* 5.9 0.2 - - + -
116B VAL* 4.1 14.4 - - + -
125B MET* 3.7 36.1 - - + -
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Residues in contact with TRP 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 HIS* 3.0 61.8 + + - +
46B SER* 3.2 6.9 + - - +
48B LEU* 1.3 76.2 - - - +
50B SER* 1.3 59.3 + - - +
51B LYS 3.1 6.6 + - - +
52B LYS* 4.7 2.1 + - - -
56B LEU* 3.5 46.3 - - + +
57B GLN* 3.7 28.8 + - - -
58B PRO* 3.9 17.7 - - + -
69B VAL* 4.8 4.3 - - + +
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Residues in contact with SER 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 SER 2.9 12.4 + - - -
47B PHE* 2.7 24.1 + - - -
49B TRP* 1.3 76.4 - - - +
51B LYS* 1.3 61.9 + - - +
52B LYS* 3.4 7.0 + - - +
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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