Contacts of the helix formed by residues 30 - 43 (chain C) in PDB entry 1UHG
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 CYS 30 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TYR* 1.3 72.9 - - - +
31C PRO* 1.4 67.8 - - - +
32C ILE* 3.6 9.2 - - - -
33C ALA* 3.2 19.4 + - + -
34C ILE* 3.1 25.6 + - - +
99C PHE* 4.2 0.4 - - - -
178C ILE* 3.3 49.8 - - + -
328C HIS* 3.0 14.6 + - + -
330C ALA* 4.4 0.2 - - - +
377C LEU 3.1 18.8 - - - +
378C PHE* 3.8 7.9 - - + -
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Residues in contact with PRO 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C SER* 4.3 7.9 - - - +
10C PHE* 4.5 8.5 - - + -
11C CYS* 3.6 42.8 - - + -
29C TYR* 3.4 20.8 - - + +
30C CYS* 1.4 81.4 - - - +
32C ILE* 1.3 56.9 + - - +
34C ILE* 3.1 12.6 + - + +
35C MET* 2.9 35.9 + - - +
376C VAL* 3.9 12.3 - - + +
377C LEU 3.3 20.4 - - - +
378C PHE* 3.9 2.2 - - - -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.3 10.1 - - + -
7C SER* 4.7 5.6 - - - -
30C CYS* 3.6 17.0 - - - -
31C PRO* 1.3 79.7 - - - +
33C ALA* 1.3 68.1 + - - +
35C MET* 3.3 7.3 + - - +
36C SER* 3.0 23.0 + - - -
83C LEU* 3.4 28.1 - - + +
86C ILE* 4.1 31.0 - - + -
87C LEU* 4.0 21.0 - - + +
99C PHE* 4.5 5.6 - - + -
375C ALA* 4.7 6.1 - - + -
376C VAL 3.8 13.8 + - - +
377C LEU* 3.9 19.5 - - + +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 3.2 28.6 + - + +
32C ILE* 1.3 83.5 - - + +
34C ILE* 1.3 63.7 + - - +
36C SER* 2.8 23.5 + - - -
37C ALA 3.1 6.2 + - - -
87C LEU* 5.0 3.6 - - + -
99C PHE* 5.5 0.4 - - + -
101C LEU* 4.0 24.0 - - + -
176C ASN* 3.2 21.1 + - - +
178C ILE* 4.3 4.7 - - + -
328C HIS* 4.3 1.8 - - + -
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.7 27.1 - - + -
14C VAL* 5.1 8.5 - - + -
29C TYR* 4.4 14.1 - - + -
30C CYS 3.1 18.7 + - - +
31C PRO* 3.1 8.6 + - + +
33C ALA* 1.3 75.9 - - - +
35C MET* 1.3 64.3 + - - +
37C ALA* 3.2 2.8 + - - +
38C LEU* 3.0 37.2 + - + +
176C ASN* 3.7 6.5 - - - +
293C LEU* 4.3 25.1 - - + -
297C LEU* 5.1 2.9 - - + -
328C HIS* 3.6 37.7 - - + +
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Residues in contact with MET 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.1 22.9 - - + -
6C ALA* 4.3 7.6 - - + +
7C SER* 3.7 38.6 - - - +
10C PHE* 3.5 23.1 - - + -
31C PRO 2.9 21.3 + - - +
32C ILE* 3.7 10.8 - - - +
33C ALA 3.3 0.2 - - - -
34C ILE* 1.3 77.5 - - - +
36C SER* 1.3 57.0 + - - +
38C LEU* 3.4 1.1 + - - +
39C ALA* 2.8 29.5 + - - +
57C VAL* 3.6 34.8 - - + +
59C PHE* 3.6 9.8 - - + -
62C LEU* 4.4 7.6 - - + -
83C LEU* 3.9 11.2 - - + -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE 3.0 9.6 + - - -
33C ALA* 2.8 22.9 + - - -
35C MET* 1.3 75.2 - - - +
37C ALA* 1.3 64.5 + - - +
39C ALA* 3.3 3.2 + - - +
40C MET* 3.1 20.6 + - - +
83C LEU* 3.6 17.0 - - - +
87C LEU* 3.3 34.2 - - - +
101C LEU* 4.7 5.4 - - - +
103C SER* 4.7 2.9 + - - -
125C TYR* 3.7 18.3 - - - -
176C ASN* 4.7 1.4 + - - -
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA 3.1 1.6 + - - -
34C ILE* 3.2 7.4 + - - +
36C SER* 1.3 82.0 + - - +
38C LEU* 1.3 69.2 + - + +
40C MET* 3.1 20.7 + - - +
41C VAL* 3.2 16.5 + - - +
103C SER* 3.6 12.1 - - - +
174C LEU* 4.1 20.0 - - + +
176C ASN* 3.6 28.7 - - + +
293C LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.0 30.5 + - + +
35C MET* 3.9 4.3 - - - +
37C ALA* 1.3 80.4 - - + +
39C ALA* 1.3 57.6 + - - +
41C VAL* 3.3 12.1 + - + +
42C TYR* 2.8 30.3 + - - +
53C ILE* 4.1 24.8 - - + +
57C VAL* 4.2 23.3 - - + -
59C PHE* 4.1 2.2 - - + -
174C LEU* 4.1 17.9 - - + -
293C LEU* 5.0 3.1 - - + -
297C LEU* 4.2 25.4 - - + -
302C ILE* 4.6 11.9 - - + -
305C VAL* 5.8 2.7 - - + -
306C PHE* 6.0 1.3 - - + -
323C ILE* 5.8 2.9 - - + -
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET 2.8 18.8 + - - +
36C SER 3.6 3.1 - - - +
37C ALA 3.2 0.2 - - - -
38C LEU* 1.3 77.5 - - - +
40C MET* 1.3 60.8 + - - +
42C TYR* 3.3 5.4 - - - +
43C LEU* 3.2 27.0 + - - +
59C PHE* 3.6 16.8 - - + -
65C PHE* 4.2 3.1 - - + -
80C HIS* 3.7 13.9 - - + +
83C LEU* 4.0 8.3 - - + -
125C TYR* 3.3 23.1 - - - +
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER 3.1 14.1 + - - +
37C ALA* 3.3 10.3 - - - +
39C ALA* 1.3 75.2 - - - +
41C VAL* 1.3 63.3 - - - +
43C LEU* 3.6 11.6 - - - +
103C SER* 4.2 27.4 - - - +
104C ARG* 5.1 1.6 - - - +
105C LEU* 4.4 11.7 - - + +
117C TYR* 2.8 35.6 + - - +
121C VAL* 4.0 13.5 - - + -
125C TYR* 3.8 33.6 - - + -
128C GLY* 3.3 40.6 - - - +
174C LEU* 5.6 1.3 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA 3.2 13.0 + - - +
38C LEU* 3.5 13.2 - - + +
40C MET* 1.3 74.4 - - - +
42C TYR* 1.3 68.7 + - - +
44C GLY* 2.9 14.7 + - - -
45C ALA* 3.4 7.4 + - - +
53C ILE* 4.0 19.5 - - + -
105C LEU* 3.9 34.8 - - + -
117C TYR* 4.4 1.1 - - - -
172C MET* 5.8 0.7 - - + -
174C LEU* 4.1 9.4 - - + -
305C VAL* 4.1 9.2 - - + -
312C LEU* 4.2 12.5 - - + +
315C ILE* 4.5 3.9 - - + +
323C ILE* 4.0 24.5 - - + -
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 2.8 17.5 + - - +
39C ALA* 3.3 12.3 - - - +
41C VAL* 1.3 77.7 - - - +
43C LEU* 1.3 63.4 + - - +
44C GLY 3.1 1.2 + - - -
45C ALA* 3.1 14.3 + - - +
50C ARG* 2.9 76.0 + - + +
53C ILE* 4.0 17.7 - - + -
54C ASN* 3.3 33.3 + - + +
59C PHE* 3.9 18.4 - + + -
65C PHE* 4.5 13.4 - + + +
66C GLY* 5.1 6.0 + - - -
70C GLU* 3.4 23.1 - - - -
80C HIS* 4.5 9.2 - - - -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA 3.2 15.0 + - - +
40C MET* 3.6 12.3 - - - +
41C VAL 3.1 0.8 + - - -
42C TYR* 1.3 80.5 - - + +
44C GLY* 1.3 57.3 + - - +
45C ALA 4.8 0.9 - - - +
46C LYS* 5.2 6.4 + - - -
50C ARG* 4.5 1.2 + - - -
70C GLU* 3.5 42.9 - - + +
79C VAL* 5.0 0.9 - - + -
80C HIS* 3.7 16.6 - - + +
117C TYR* 4.0 11.2 - - + -
120C CYS* 3.5 35.7 - - + -
121C VAL* 4.9 7.9 - - + -
124C LEU* 3.8 14.8 - - + -
125C TYR* 4.1 16.6 - - + -
314C GLY* 5.3 0.5 - - - -
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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