Contacts of the helix formed by residues 38 - 46 (chain A) in PDB entry 1HWG
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 LYS 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE 4.0 1.0 + - - -
37A PRO* 1.3 69.9 - - - +
39A GLU* 1.3 65.6 + - + +
41A LYS* 3.1 11.2 + - - -
42A TYR* 2.8 54.4 + - + +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 2.8 27.9 + - + +
38A LYS* 1.3 77.0 - - + +
40A GLN* 1.3 57.8 + - + +
42A TYR* 3.1 7.7 + - - +
43A SER* 2.8 33.7 + - - -
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A TYR 4.2 7.1 + - - -
36A ILE* 4.2 16.8 - - + -
37A PRO* 2.8 38.0 + - + +
39A GLU* 1.3 75.5 - - + +
41A LYS* 1.3 61.4 + - - +
43A SER* 3.7 9.0 - - - +
44A PHE* 2.9 32.1 + - - +
154A ASP* 5.5 0.3 - - - +
156A LEU* 4.1 20.3 - - - +
157A LEU* 4.3 11.9 - - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 4.4 7.3 + - - -
32A GLU* 3.8 22.2 - - - +
36A ILE* 4.0 9.8 - - + +
37A PRO 3.1 6.9 + - - +
38A LYS* 3.1 17.6 + - - +
40A GLN* 1.3 78.3 - - - +
42A TYR* 1.3 70.8 + - + +
44A PHE* 3.4 4.7 - - - +
45A LEU* 3.0 47.7 + - + +
160A TYR* 3.5 18.5 + - - +
164A TYR* 5.2 1.6 - - - -
122B CYS 4.1 14.6 - - - -
123B PHE* 5.7 0.2 - - - -
127B GLU* 3.0 33.4 + - - -
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 2.8 35.9 + - + +
39A GLU* 3.4 9.6 - - - +
41A LYS* 1.3 84.9 - - + +
43A SER* 1.3 67.6 + - - +
45A LEU* 3.4 3.5 + - - +
46A GLN* 3.3 29.6 + - - +
120B GLU* 3.8 29.2 - - - +
121B LYS* 2.9 30.0 + - + +
122B CYS* 3.4 48.5 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU 2.8 20.5 + - - -
40A GLN* 3.7 8.8 - - - +
42A TYR* 1.3 75.3 - - - +
44A PHE* 1.3 53.2 + - - +
46A GLN* 3.2 12.7 + - - +
47A ASN* 2.8 38.6 + - - +
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN 2.9 19.4 + - - +
41A LYS* 3.4 5.8 - - - +
43A SER* 1.3 75.7 - - - +
45A LEU* 1.3 80.5 - - + +
46A GLN 3.1 1.6 + - - -
47A ASN* 3.2 14.2 + - - -
50A THR* 3.3 51.5 - - - -
51A SER* 3.6 6.6 + - - -
157A LEU* 4.7 23.1 - - + -
160A TYR* 3.3 35.0 - + + -
161A GLY* 3.9 23.8 - - - -
164A TYR* 3.6 41.3 - + - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.0 48.4 + - + +
42A TYR 3.8 4.7 - - - +
43A SER 3.4 0.2 - - - -
44A PHE* 1.3 83.4 - - + +
46A GLN* 1.3 57.8 + - - +
47A ASN 3.6 0.2 - - - -
51A SER* 3.2 22.7 - - - -
164A TYR* 3.5 34.5 - - + +
71B ARG* 4.4 0.5 + - - -
76B TRP* 3.3 17.8 - - + -
106B PRO* 3.8 25.2 - - + +
122B CYS* 4.1 30.7 - - + -
123B PHE* 4.2 7.4 - - - +
124B SER* 5.0 0.7 - - - +
127B GLU* 4.7 2.2 - - - +
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.3 25.4 + - - +
43A SER* 3.5 10.3 - - - +
45A LEU* 1.3 76.0 - - - +
47A ASN* 1.3 66.1 - - - +
48A PRO 3.9 0.5 - - - -
76B TRP* 3.5 19.0 + - + -
77B THR* 3.6 34.4 + - + +
80B TRP* 5.6 3.8 - - - -
108B CYS* 3.9 15.2 - - - +
120B GLU* 3.9 26.3 + - - +
122B CYS* 4.6 0.3 - - - -
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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