Contacts of the helix formed by residues 30 - 43 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 1.3 75.7 - - - +
31A PRO* 1.3 67.7 - - - +
32A ILE* 3.6 10.8 - - - -
33A ALA* 3.2 25.9 + - + -
34A ILE* 3.2 24.6 + - - +
99A PHE* 4.2 7.0 - - - -
178A ILE* 3.6 24.7 - - + -
328A HIS* 3.0 9.6 + - + -
330A ALA* 4.2 0.4 - - - +
377A LEU 3.2 17.9 - - - +
378A PHE* 3.7 18.4 - - + -
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Residues in contact with PRO 31 (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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7A SER* 4.4 7.9 - - - +
10A PHE* 4.1 8.2 - - + -
11A CYS* 3.6 33.0 - - + -
29A TYR* 3.2 37.9 - - + +
30A CYS* 1.3 82.2 - - - +
32A ILE* 1.3 61.5 + - - +
34A ILE* 3.2 9.5 + - + +
35A MET* 3.0 29.7 + - - +
376A VAL* 4.0 12.6 - - + +
377A LEU 3.4 16.6 - - - +
378A PHE* 3.9 2.0 - - - -
379A PHE 4.2 0.2 - - - +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.1 22.0 - - + -
7A SER* 4.5 10.7 - - - -
30A CYS* 3.6 16.6 - - - -
31A PRO* 1.3 79.5 - - - +
33A ALA* 1.3 66.6 + - - +
35A MET* 3.4 8.1 + - - +
36A SER* 3.1 21.7 + - - -
83A LEU* 3.3 30.6 - - + +
86A ILE* 4.5 14.6 - - + -
87A LEU* 4.2 20.8 - - + +
99A PHE* 4.6 5.2 - - + -
375A ALA* 4.8 3.8 - - + -
376A VAL 3.7 12.2 + - - +
377A LEU* 4.0 24.2 - - + +
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Residues in contact with ALA 33 (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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30A CYS* 3.2 27.9 + - + +
32A ILE* 1.3 80.9 - - + +
34A ILE* 1.3 64.8 + - - +
36A SER* 3.2 8.0 + - - -
37A ALA 3.1 18.7 + - - -
87A LEU* 5.0 4.0 - - - -
99A PHE* 5.2 1.8 - - + -
101A LEU* 3.9 25.4 - - + -
176A ASN* 3.3 21.3 + - - +
178A ILE* 4.8 2.9 - - + -
328A HIS* 4.5 1.6 - - + -
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Residues in contact with ILE 34 (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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10A PHE* 3.7 28.0 - - + -
14A VAL* 5.1 8.5 - - + -
29A TYR* 4.3 17.7 - - + -
30A CYS 3.2 12.9 + - - +
31A PRO* 3.2 8.8 + - + +
33A ALA* 1.3 75.0 - - - +
35A MET* 1.3 63.1 + - - +
37A ALA* 3.4 3.6 + - + +
38A LEU* 3.1 34.2 + - + +
176A ASN* 3.7 6.1 - - - +
293A LEU* 4.3 27.8 - - + -
297A LEU* 4.9 1.8 - - + -
328A HIS* 3.5 40.4 - - + +
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Residues in contact with MET 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.2 17.0 - - + -
6A ALA* 3.9 20.6 - - + +
7A SER* 3.7 30.7 - - - +
10A PHE* 3.5 21.1 - - + -
31A PRO 3.0 20.2 + - - +
32A ILE* 3.6 10.5 - - - +
34A ILE* 1.3 77.5 - - - +
36A SER* 1.3 51.8 + - - +
38A LEU* 3.3 1.5 + - - -
39A ALA* 2.7 35.3 + - - +
57A VAL* 3.8 38.4 - - + +
59A PHE* 3.7 9.4 - - + -
62A LEU* 5.0 3.6 - - + -
83A LEU* 3.7 12.3 - - + -
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Residues in contact with SER 36 (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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32A ILE 3.1 7.4 + - - -
33A ALA* 3.2 9.4 + - - -
35A MET* 1.3 77.4 - - - +
37A ALA* 1.3 61.2 + - - +
39A ALA* 3.3 3.2 + - - +
40A MET* 3.1 22.2 + - - +
83A LEU* 3.7 12.3 - - - +
87A LEU* 3.2 36.0 - - - +
101A LEU* 5.3 3.4 - - - -
103A SER* 5.3 1.8 + - - -
125A TYR* 3.5 22.6 - - - -
176A ASN* 5.8 0.4 - - - -
401A SO4 3.7 9.3 + - - -
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Residues in contact with ALA 37 (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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33A ALA 3.1 6.0 + - - +
34A ILE* 3.7 8.5 - - + +
36A SER* 1.3 77.1 - - - +
38A LEU* 1.3 64.0 + - + +
40A MET* 3.3 10.4 + - - +
41A VAL* 3.3 24.2 + - - +
103A SER* 3.7 13.1 + - - +
174A LEU* 4.0 27.6 - - + +
176A ASN* 3.7 28.3 - - + +
293A LEU* 5.9 1.8 - - + -
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Residues in contact with LEU 38 (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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10A PHE* 4.3 3.1 - - + -
34A ILE* 3.1 33.4 + - + +
35A MET 3.8 3.8 - - - +
37A ALA* 1.3 75.8 - - + +
39A ALA* 1.3 62.6 + - - +
41A VAL* 3.1 9.7 + - + +
42A TYR* 2.8 29.1 + - - +
53A ILE* 4.4 15.0 - - + +
57A VAL* 3.6 32.5 - - + -
59A PHE* 4.2 2.9 - - + -
174A LEU* 5.0 11.9 - - + -
293A LEU* 6.4 0.9 - - + -
297A LEU* 3.8 38.4 - - + -
302A ILE* 4.3 12.8 - - + -
305A VAL* 6.1 1.8 - - + -
306A PHE* 5.7 2.0 - - + -
323A ILE* 5.9 3.6 - - + -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET 2.7 21.4 + - - +
36A SER 3.3 3.1 + - - +
38A LEU* 1.3 72.6 - - - +
40A MET* 1.3 63.1 + - - +
42A TYR* 3.3 3.6 + - - +
43A LEU* 3.2 17.7 + - - +
59A PHE* 3.6 21.5 - - + -
65A PHE* 3.9 6.7 - - + -
80A HIS* 3.4 24.0 - - + +
83A LEU* 3.9 9.6 - - + -
125A TYR* 3.5 16.6 - - - +
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Residues in contact with MET 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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36A SER 3.1 12.6 + - - +
37A ALA* 3.5 12.1 - - - +
38A LEU 3.2 0.2 - - - -
39A ALA* 1.3 78.7 - - - +
41A VAL* 1.3 58.9 - - - +
43A LEU* 3.3 15.3 - - - +
103A SER* 5.1 4.5 - - - +
104A ARG* 4.3 5.8 - - - +
105A LEU* 3.6 33.7 - - + +
117A TYR* 2.9 25.4 + - - +
121A VAL* 4.4 9.0 - - + -
125A TYR* 3.9 39.9 + - + -
128A GLY* 3.2 45.3 - - - +
129A LEU* 5.2 0.4 - - + -
174A LEU* 4.9 5.4 - - + -
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Residues in contact with VAL 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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37A ALA 3.3 12.5 + - - +
38A LEU* 3.1 12.7 + - + +
40A MET* 1.3 71.9 - - - +
42A TYR* 1.3 65.7 + - - +
43A LEU 2.9 6.0 + - - -
44A GLY* 2.9 14.2 + - - -
45A ALA* 3.4 6.8 + - - +
53A ILE* 4.2 10.1 - - + -
105A LEU* 3.8 26.0 - - + -
117A TYR* 4.2 4.9 - - - -
172A MET* 6.2 0.2 - - + -
174A LEU* 4.5 7.9 - - + -
305A VAL* 4.0 27.6 - - + -
312A LEU* 4.0 13.6 - - + +
315A ILE* 4.6 5.0 - - + +
323A ILE* 4.0 20.6 - - + -
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Residues in contact with TYR 42 (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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38A LEU 2.8 17.3 + - - +
39A ALA* 3.3 8.7 - - - +
41A VAL* 1.3 77.5 - - - +
43A LEU* 1.3 60.3 + - - +
44A GLY 3.2 0.7 + - - -
45A ALA* 3.4 13.9 + - - +
50A ARG* 2.5 71.6 + - + -
53A ILE* 3.7 21.5 - - + +
54A ASN* 3.4 33.2 + - + +
59A PHE* 3.7 22.9 - + + -
65A PHE* 4.5 3.6 - + - -
66A GLY* 5.3 2.9 + - - -
70A GLU* 3.3 38.3 + - - -
80A HIS* 4.5 5.8 - - - -
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Residues in contact with LEU 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 ALA 3.2 12.3 + - - +
40A MET* 3.3 13.5 - - - +
41A VAL 2.9 0.6 + - - -
42A TYR* 1.3 77.8 - - - +
44A GLY* 1.3 56.4 + - - +
45A ALA 3.5 1.1 - - - +
46A LYS* 5.4 4.0 + - - -
50A ARG* 5.4 3.3 + - - +
70A GLU* 3.8 17.9 - - + +
73A CYS* 4.0 11.0 - - + -
79A VAL* 4.6 4.3 - - + -
80A HIS* 3.3 25.4 - - + +
117A TYR* 3.9 12.8 - - + -
120A CYS* 3.1 33.2 - - - -
121A VAL* 5.0 2.7 - - + -
124A LEU* 4.1 1.3 - - + -
125A TYR* 3.9 29.4 - - + -
314A GLY* 5.3 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