Contacts of the helix formed by residues 36 - 51 (chain B) in PDB entry 4HFG
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 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 3.8 42.3 - + + +
207A UNX 3.7 19.1 - - - -
33B HIS* 2.9 21.8 + - + +
34B ARG 2.8 1.8 - - - -
35B LYS* 1.3 111.8 + - + +
37B ALA* 1.3 63.1 + - - +
38B GLY 3.0 5.1 + - - -
39B PRO* 3.3 13.3 - - + +
40B ILE* 3.0 28.6 + - + +
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Residues in contact with ALA 37 (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 ARG 3.0 15.8 + - - +
35B LYS 3.6 1.0 - - - -
36B HIS* 1.3 77.0 - - - +
38B GLY* 1.3 61.7 + - - +
40B ILE* 3.4 0.8 + - - +
41B VAL* 3.0 29.8 + - - +
76B GLU* 3.7 21.3 - - + -
77B PHE* 3.7 30.3 - - + -
79B ARG* 5.9 0.2 - - - +
80B GLU* 3.8 14.1 - - + -
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS 3.0 0.4 + - - -
37B ALA* 1.3 81.4 - - - +
39B PRO* 1.3 70.7 - - - +
41B VAL* 3.3 3.3 + - - +
42B SER* 3.2 22.9 + - - -
80B GLU* 3.7 25.3 - - - +
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Residues in contact with PRO 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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4A PHE* 4.6 14.1 - - + -
6A GLU* 4.0 19.7 - - - +
36B HIS* 3.3 17.7 - - + +
38B GLY* 1.3 89.7 - - - +
40B ILE* 1.3 61.4 + - - +
42B SER* 3.2 8.7 + - - +
43B VAL* 3.0 29.2 + - - +
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Residues in contact with ILE 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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4A PHE* 3.4 30.5 - - + -
9A LEU* 3.7 14.9 - - + +
30B LEU* 4.0 35.7 - - + +
33B HIS* 3.6 23.8 - - + +
36B HIS* 3.0 22.1 + - + +
37B ALA 3.6 4.3 - - - +
39B PRO* 1.3 75.4 - - - +
41B VAL* 1.3 61.2 + - + +
43B VAL 3.4 0.3 + - - -
44B TRP* 2.9 30.8 + - + +
77B PHE* 3.8 32.5 - - + -
81B PHE* 5.6 2.9 - - + -
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Residues in contact with VAL 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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37B ALA 3.0 20.6 + - - +
38B GLY 3.8 3.8 - - - +
40B ILE* 1.3 76.9 - - - +
42B SER* 1.3 53.1 + - - +
44B TRP* 3.5 6.8 - - - +
45B HIS* 2.8 34.3 + - - +
77B PHE* 4.4 5.6 - - + -
80B GLU* 3.7 30.5 - - + +
81B PHE* 3.8 35.0 - - + -
84B VAL* 3.6 36.8 - - + -
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Residues in contact with SER 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 GLY 3.2 14.6 + - - -
39B PRO* 3.5 11.9 - - - +
41B VAL* 1.3 77.6 - - - +
43B VAL* 1.3 64.1 + - - +
45B HIS* 3.4 5.9 + - - +
46B ARG* 3.0 34.3 + - - +
84B VAL* 6.1 0.9 - - - -
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Residues in contact with VAL 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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6A GLU* 3.6 36.6 - - + +
9A LEU* 3.5 33.2 - - + -
10A GLU* 3.7 29.4 - - + +
13A LEU* 3.9 6.1 - - + -
39B PRO 3.0 14.2 + - - +
42B SER* 1.3 74.6 - - - +
44B TRP* 1.3 67.0 + - - +
46B ARG* 3.3 19.3 + - - +
47B GLU* 2.9 30.2 + - + +
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Residues in contact with TRP 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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9A LEU* 5.5 0.9 - - + -
13A LEU* 4.1 15.5 - - + +
30B LEU* 6.0 2.5 - - + -
40B ILE* 2.9 21.4 + - + +
41B VAL* 3.2 10.7 + - - +
43B VAL* 1.3 75.6 - - - +
45B HIS* 1.3 82.7 + - + +
47B GLU* 3.8 0.5 - - - -
48B LEU* 2.8 37.9 + - + +
59B PHE* 3.0 61.7 + + + +
60B LEU* 3.9 11.7 - - + -
62B LEU* 4.0 21.0 - - + +
63B ALA* 3.8 12.9 - - + +
81B PHE* 3.6 28.3 - + + -
84B VAL* 3.8 22.4 - - + -
85B LEU* 4.4 3.1 - - + -
88B ALA* 3.7 27.1 - - + -
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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 VAL 2.8 20.8 + - - +
42B SER* 3.7 6.3 - - - +
43B VAL 3.2 0.2 - - - -
44B TRP* 1.3 94.6 - + + +
46B ARG* 1.3 61.8 + - - +
48B LEU* 3.5 11.4 + - + +
49B ARG* 3.2 33.3 + - + +
84B VAL* 3.7 34.8 + - + +
87B ASP* 2.7 38.4 + - + +
88B ALA* 4.4 1.5 + - + -
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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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6A GLU* 4.3 7.1 + - - -
10A GLU* 3.7 20.2 + - - -
42B SER* 3.0 27.3 + - - +
43B VAL* 3.8 23.3 - - - +
45B HIS* 1.3 75.6 - - - +
47B GLU* 1.3 75.0 + - - +
49B ARG* 3.2 18.3 + - - +
50B LYS* 3.3 25.5 + - + +
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Residues in contact with GLU 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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10A GLU* 4.1 26.7 - - + +
13A LEU* 4.0 19.5 - - + +
14A SER* 6.1 0.5 - - - -
43B VAL* 2.9 27.1 + - + +
44B TRP 3.9 0.2 - - - +
46B ARG* 1.3 92.0 + - - +
48B LEU* 1.3 67.0 + - - +
50B LYS* 2.9 29.6 + - - +
51B ALA* 3.0 14.7 + - - +
59B PHE* 3.8 20.6 - - + -
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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 TRP* 2.8 50.9 + - + +
45B HIS* 3.5 10.8 - - + +
47B GLU* 1.3 72.6 - - - +
49B ARG* 1.3 58.1 + - + +
50B LYS 3.2 0.9 + - - -
51B ALA* 3.2 6.0 + - - +
56B LYS* 2.9 62.4 + - + +
59B PHE* 3.4 22.4 - - + -
60B LEU* 5.4 0.2 - - + -
88B ALA* 4.0 20.0 - - + +
91B HIS* 4.1 10.3 - - + -
92B VAL* 3.8 17.0 - - + -
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Residues in contact with ARG 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* 3.2 26.5 + - + +
46B ARG* 3.2 13.5 + - + +
47B GLU 3.1 1.2 - - - -
48B LEU* 1.3 77.3 - - + +
50B LYS* 1.3 61.8 + - + +
51B ALA 3.6 0.2 - - - -
56B LYS* 3.8 7.8 + - - -
87B ASP* 2.7 41.4 + - - -
91B HIS* 3.1 41.5 + - + +
94B ARG* 4.1 5.1 - - - +
204B UNX 2.8 29.3 - - - -
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Residues in contact with LYS 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* 3.3 24.1 + - + +
47B GLU* 2.9 28.0 + - - +
49B ARG* 1.3 82.4 - - + +
51B ALA* 1.3 62.7 + - - +
52B LYS* 3.7 1.4 + - - +
56B LYS* 4.4 0.2 - - - -
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Residues in contact with ALA 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 GLU 3.0 13.1 + - - +
48B LEU 3.2 9.4 + - - +
50B LYS* 1.3 79.6 - - - +
52B LYS* 1.3 68.8 + - - +
53B SER 3.5 0.3 + - - -
55B ARG* 4.2 10.8 - - + +
56B LYS* 2.7 33.8 + - + +
59B PHE* 3.5 28.7 - - + -
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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