Contacts of the helix formed by residues 43 - 57 (chain B) in PDB entry 1H4L
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 GLY 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 1.3 71.9 + - - +
45B PRO* 3.4 9.1 - - - +
46B SER* 3.0 17.3 + - - -
47B SER* 3.3 6.6 + - - -
242E SER* 3.1 30.8 - - - -
243E TYR 3.4 26.3 + - - -
244E PRO* 5.1 3.0 - - - +
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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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9A LYS* 5.5 9.0 - - - +
15B TYR* 3.2 43.7 - - + -
16B GLY 5.4 0.7 - - - +
35B VAL* 3.4 19.5 - - + -
36B ARG* 4.5 6.1 - - + +
43B GLY* 1.3 79.0 - - - +
45B PRO* 1.3 63.0 - - + +
47B SER* 3.2 3.5 + - - -
48B ALA* 2.9 23.4 + - - +
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Residues in contact with PRO 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.7 2.9 - - + -
36B ARG 3.8 19.1 - - - +
37B LEU* 4.3 13.9 - - + -
38B ASP 5.4 0.2 - - - +
43B GLY* 3.5 9.6 - - - +
44B VAL* 1.3 95.7 - - + +
46B SER* 1.3 51.9 + - - +
48B ALA* 3.0 9.6 + - + +
49B LEU* 2.7 40.8 + - + +
76B LEU* 6.0 1.1 - - + -
231E TYR* 3.6 5.8 - - - +
243E TYR 5.7 0.2 - - - +
245E LEU* 6.1 1.8 - - + -
258E TRP* 3.5 35.2 - - + -
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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
----------------------------------------------------------
43B GLY 3.0 11.9 + - - -
45B PRO* 1.3 79.8 - - - +
47B SER* 1.3 64.5 + - - +
49B LEU* 4.4 2.0 - - - -
50B ARG* 3.1 21.4 + - - +
231E TYR* 3.4 18.3 + - - -
235E SER* 3.2 39.6 - - - -
241E ILE 4.3 0.5 + - - -
242E SER* 3.3 7.4 - - - -
243E TYR* 3.3 27.0 + - - -
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 2.7 25.5 + - - -
43B GLY 3.3 8.7 + - - -
44B VAL* 3.2 9.1 + - - -
45B PRO 3.1 0.8 - - - -
46B SER* 1.3 78.5 + - - +
48B ALA* 1.3 66.7 + - - +
50B ARG* 3.2 13.0 + - - +
51B GLU* 2.9 19.4 + - - +
146B GLY* 2.5 30.6 + - - +
147B LEU* 5.1 2.1 - - - +
241E ILE 4.2 10.8 - - - -
242E SER* 5.0 1.1 - - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.2 21.5 + - + -
35B VAL* 4.1 21.3 - - + -
44B VAL 2.9 13.2 + - - +
45B PRO* 3.0 12.3 + - + +
47B SER* 1.3 78.2 - - - +
49B LEU* 1.3 57.4 + - - +
51B GLU* 3.2 6.5 + - - +
52B ILE* 3.0 33.9 + - + +
76B LEU* 5.1 9.9 - - + -
78B LEU* 4.7 6.6 - - + +
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Residues in contact with LEU 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 PRO 2.7 22.1 + - - +
46B SER* 3.8 5.6 - - - +
48B ALA* 1.3 70.5 - - - +
50B ARG* 1.3 64.9 + - - +
52B ILE* 3.3 10.6 + - + +
53B CYS* 3.0 27.6 + - - -
76B LEU* 4.0 24.7 - - + -
231E TYR* 3.7 29.2 - - + -
232E LEU* 3.9 20.6 - - + -
235E SER* 4.8 3.4 - - - +
258E TRP* 4.2 8.5 - - + -
261E CYS* 4.1 19.5 - - + -
262E LEU* 4.7 5.6 - - + -
265E ILE* 3.5 23.9 - - + +
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.1 19.8 + - - +
47B SER* 3.2 6.3 + - - +
49B LEU* 1.3 74.1 - - - +
51B GLU* 1.3 66.2 + - - +
53B CYS* 3.3 7.3 + - - +
54B LEU* 3.0 38.8 + - + +
125B ARG* 4.7 4.2 - - - +
145B PHE 5.2 0.6 + - - +
146B GLY 2.9 27.6 + - - -
147B LEU* 4.0 6.7 - - - +
148B ALA 2.6 28.2 + - - +
149B ARG* 4.4 7.3 - - - +
235E SER* 2.9 33.7 + - - +
236E TYR* 4.2 23.1 - - + -
238E GLY 5.8 0.6 + - - -
240E GLU 5.3 2.0 + - - -
241E ILE* 3.4 37.2 + - - +
242E SER* 5.3 0.4 - - - +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.0 32.9 + - - +
33B LYS* 3.1 19.1 + - - +
47B SER 2.9 12.4 + - - +
48B ALA* 3.2 9.1 + - - +
50B ARG* 1.3 78.4 - - - +
52B ILE* 1.3 64.5 + - + +
54B LEU* 3.8 1.8 - - - +
55B LEU* 2.8 33.7 + - + +
78B LEU* 4.9 5.9 - - + +
80B PHE* 3.4 21.0 - - + -
144B ASP* 4.0 2.6 + - - -
145B PHE* 3.5 45.5 + - + +
146B GLY 4.0 1.9 + - - -
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Residues in contact with ILE 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 ALA 3.0 15.7 + - - +
49B LEU* 3.6 24.0 - - + +
51B GLU* 1.3 76.8 - - - +
53B CYS* 1.3 64.7 + - - +
55B LEU* 3.1 1.4 + - - +
56B LYS* 2.9 37.8 + - + +
66B LEU* 4.1 14.5 - - + +
69B VAL* 3.7 35.9 - - + -
76B LEU* 4.6 5.4 - - + -
78B LEU* 3.3 33.0 - - + -
262E LEU* 4.5 6.7 - - + -
265E ILE* 3.9 20.9 - - + -
266E ASN* 5.5 1.8 - - - +
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Residues in contact with CYS 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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49B LEU 3.0 16.8 + - - +
50B ARG* 3.3 8.7 + - - +
52B ILE* 1.3 78.3 - - - +
54B LEU* 1.3 65.3 + - - +
56B LYS* 3.4 10.6 + - - +
57B GLU* 3.6 15.2 + - - +
232E LEU* 5.6 0.7 - - - -
236E TYR* 3.8 19.1 - - + -
265E ILE* 3.7 37.5 - - - -
269E SER* 4.0 10.2 + - - +
272E MET* 3.8 29.8 - - - -
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Residues in contact with LEU 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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50B ARG* 3.0 24.3 + - + +
51B GLU* 3.8 3.1 - - - +
53B CYS* 1.3 78.7 - - - +
55B LEU* 1.3 64.5 + - - +
57B GLU* 3.1 15.1 + - - +
58B LEU* 3.1 29.1 - - + +
122B VAL* 3.8 24.0 - - + -
145B PHE* 4.6 7.9 - - + +
148B ALA* 3.5 45.1 - - + +
149B ARG* 3.6 5.6 - - - +
150B ALA 4.3 6.5 - - - +
236E TYR* 3.6 33.2 - - + +
273E LEU* 4.7 2.9 - - + -
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Residues in contact with LEU 55 (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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51B GLU* 2.8 40.2 + - + +
52B ILE 3.7 2.5 - - - +
54B LEU* 1.3 73.5 - - - +
56B LYS* 1.3 64.8 + - - +
58B LEU* 3.0 26.6 + - + +
59B LYS* 4.1 8.5 + - - -
63B ILE* 4.1 16.8 - - + -
64B VAL* 4.2 13.0 - - + +
66B LEU* 4.1 21.0 - - + +
78B LEU* 6.1 0.2 - - + -
80B PHE* 3.5 32.5 - - + -
144B ASP 5.9 0.4 - - - +
145B PHE* 3.8 35.2 - - + -
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Residues in contact with LYS 56 (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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52B ILE* 2.9 35.3 + - + +
53B CYS 3.7 3.1 - - - +
54B LEU 3.3 0.2 - - - -
55B LEU* 1.3 72.1 - - - +
57B GLU* 1.3 63.9 + - - +
59B LYS* 3.5 25.4 - - - +
66B LEU* 4.5 9.2 - - + -
69B VAL* 6.1 2.2 - - - -
265E ILE* 4.1 12.1 - - + -
266E ASN* 2.6 48.2 + - - +
269E SER* 3.5 29.2 - - - +
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Residues in contact with GLU 57 (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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53B CYS 3.8 5.4 - - - +
54B LEU* 3.1 7.0 + - - +
55B LEU 3.0 0.8 - - - -
56B LYS* 1.3 85.1 - - - +
58B LEU* 1.3 60.2 + - - +
59B LYS* 3.9 4.0 + - - -
116B PHE* 4.9 0.3 - - - -
120B ARG* 2.8 48.7 + - - +
269E SER* 2.4 45.8 + - - +
270E SER* 3.2 29.8 + - - -
273E LEU* 3.8 18.2 - - + -
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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