Contacts of the helix formed by residues 30 - 43 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 1.3 74.2 - - - +
31B PRO* 1.3 69.0 - - - +
32B ILE* 3.2 17.9 - - - -
33B ALA* 3.1 26.2 + - - -
34B ILE* 3.2 16.2 + - - +
99B PHE* 4.1 11.2 - - - -
178B ILE* 3.7 17.0 - - + -
328B HIS* 3.1 10.0 + - + -
330B ALA* 4.4 0.2 - - - +
377B LEU 3.1 19.5 - - - +
378B PHE* 3.6 23.1 - - + -
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Residues in contact with PRO 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 4.5 4.0 - - - +
10B PHE* 4.1 10.7 - - + -
11B CYS* 3.7 43.1 - - + +
29B TYR* 3.4 24.0 - - + +
30B CYS* 1.3 84.0 - - - +
32B ILE* 1.3 61.1 + - - +
34B ILE* 3.2 12.3 + - + +
35B MET* 3.0 31.6 + - - +
376B VAL* 3.8 17.7 - - + +
377B LEU 3.5 11.4 - - - +
378B PHE* 4.1 2.9 - - - -
379B PHE 4.2 1.6 - - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.4 10.8 - - + -
7B SER* 4.2 23.1 - - - -
30B CYS* 3.2 18.3 + - - -
31B PRO* 1.3 80.3 - - - +
33B ALA* 1.3 66.8 + - - +
35B MET* 3.5 5.7 + - - +
36B SER* 3.1 21.1 + - - -
83B LEU* 3.5 24.2 - - + +
86B ILE* 4.4 11.4 - - + -
87B LEU* 3.6 32.5 - - + +
99B PHE* 4.3 5.6 - - + -
375B ALA* 4.5 7.4 - - + -
376B VAL 3.7 13.3 + - - +
377B LEU* 4.1 19.3 - - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 3.1 26.1 + - + +
32B ILE* 1.3 79.8 - - + +
34B ILE* 1.3 65.8 + - - +
36B SER* 3.2 8.3 + - - -
37B ALA 3.0 18.0 + - - -
87B LEU* 5.1 2.9 - - - -
99B PHE* 5.1 2.0 - - + -
101B LEU* 4.0 20.0 - - + -
176B ASN* 3.1 28.8 + - - +
178B ILE* 4.6 4.3 - - + -
328B HIS* 4.4 1.6 - - + -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.7 27.4 - - + -
14B VAL* 5.1 8.5 - - + -
29B TYR* 4.3 12.3 - - + -
30B CYS 3.2 14.6 + - - +
31B PRO* 3.2 10.5 + - + +
33B ALA* 1.3 76.2 - - - +
35B MET* 1.3 63.9 + - - +
37B ALA* 3.2 4.1 + - - +
38B LEU* 3.0 33.1 + - + +
176B ASN* 3.7 6.7 - - - +
293B LEU* 4.2 28.5 - - + -
297B LEU* 5.0 3.4 - - + -
328B HIS* 3.4 40.4 - - + +
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Residues in contact with MET 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.9 23.1 - - + -
6B ALA* 4.3 6.1 - - + +
7B SER* 3.6 37.7 - - - +
10B PHE* 3.4 24.0 - - + -
31B PRO 3.0 21.5 + - - +
32B ILE* 3.7 11.9 - - - +
33B ALA 3.2 0.2 - - - -
34B ILE* 1.3 76.3 - - - +
36B SER* 1.3 57.6 + - - +
38B LEU* 3.4 4.7 + - - -
39B ALA* 2.8 31.4 + - - +
57B VAL* 4.2 29.8 - - + +
59B PHE* 3.6 11.1 - - + -
62B LEU* 4.8 3.1 - - + -
83B LEU* 3.9 10.8 - - + -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE 3.1 14.9 + - - -
33B ALA* 3.4 12.8 - - - -
34B ILE 3.2 0.2 - - - -
35B MET* 1.3 75.9 - - - +
37B ALA* 1.3 63.0 + - - +
39B ALA* 3.2 3.5 + - - +
40B MET* 3.1 22.7 + - - +
83B LEU* 4.0 13.6 - - - +
87B LEU* 4.5 18.5 - - - +
101B LEU* 4.8 9.6 - - - +
103B SER* 5.2 4.0 + - - -
125B TYR* 3.6 22.7 - - - -
176B ASN* 5.6 0.2 - - - -
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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
----------------------------------------------------------
33B ALA 3.0 6.3 + - - -
34B ILE* 3.2 7.6 + - + +
36B SER* 1.3 76.8 - - - +
38B LEU* 1.3 65.4 + - + +
40B MET* 3.2 20.1 + - - +
41B VAL* 3.2 18.0 + - - +
103B SER* 3.9 11.8 + - - +
174B LEU* 4.0 28.7 - - + -
176B ASN* 3.8 24.0 - - - +
293B LEU* 6.0 1.3 - - + -
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Residues in contact with LEU 38 (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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10B PHE* 4.2 3.8 - - + -
34B ILE* 3.0 32.9 + - + +
35B MET 3.9 3.4 - - - +
37B ALA* 1.3 77.2 - - + +
39B ALA* 1.3 52.0 + - - +
41B VAL* 3.2 11.9 + - + +
42B TYR* 2.7 35.7 + - - +
53B ILE* 4.4 12.4 - - + +
57B VAL* 3.6 32.8 - - + -
59B PHE* 4.1 4.2 - - + -
174B LEU* 4.9 13.5 - - + -
293B LEU* 6.3 0.4 - - + -
297B LEU* 3.9 37.5 - - + -
302B ILE* 4.3 9.4 - - + -
305B VAL* 6.4 1.8 - - + -
306B PHE* 6.1 1.3 - - + -
323B ILE* 5.8 3.6 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B MET 2.8 22.6 + - - +
36B SER 3.2 3.1 + - - +
38B LEU* 1.3 72.2 - - - +
40B MET* 1.3 61.6 + - - +
42B TYR* 3.3 4.0 - - - +
43B LEU* 3.2 27.0 + - - +
59B PHE* 3.5 22.4 - - + -
65B PHE* 4.5 1.1 - - + -
80B HIS* 3.6 14.0 - - + +
83B LEU* 3.9 11.2 - - + -
125B TYR* 3.4 19.7 - - - +
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Residues in contact with MET 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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36B SER 3.1 11.9 + - - +
37B ALA* 3.2 15.2 + - - +
39B ALA* 1.3 78.0 - - - +
41B VAL* 1.3 54.9 + - - +
43B LEU* 3.7 6.8 - - + +
103B SER* 5.0 3.8 - - - +
104B ARG* 4.4 7.2 - - - +
105B LEU* 3.8 26.9 - - + +
117B TYR* 2.7 39.3 + - - +
121B VAL* 4.4 10.5 - - + -
125B TYR* 3.5 49.0 - - + -
128B GLY* 3.5 36.3 - - - +
129B LEU* 5.9 0.2 - - - -
174B LEU* 4.8 6.1 - - + -
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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
----------------------------------------------------------
37B ALA 3.2 16.4 + - - +
38B LEU* 3.6 12.3 - - + +
40B MET* 1.3 72.8 - - - +
42B TYR* 1.3 67.6 + - - +
43B LEU 3.1 2.0 - - - -
44B GLY* 3.0 15.2 + - - -
45B ALA* 3.3 8.3 + - - +
53B ILE* 4.3 10.3 - - + -
105B LEU* 4.0 26.7 - - + -
117B TYR* 4.2 4.5 - - - -
174B LEU* 4.9 6.3 - - + -
305B VAL* 4.1 6.5 - - + -
312B LEU* 4.1 23.1 - - + -
315B ILE* 4.5 5.8 - - + +
323B ILE* 4.1 29.6 - - + -
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Residues in contact with TYR 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 LEU 2.7 20.9 + - - +
39B ALA 3.3 7.9 - - - +
41B VAL* 1.3 74.0 - - - +
43B LEU* 1.3 57.7 + - - +
45B ALA* 3.0 15.4 + - - +
50B ARG* 2.7 97.1 + - + +
53B ILE* 3.7 21.3 - - + +
54B ASN* 2.9 37.3 + - + +
59B PHE* 3.7 25.8 - + + -
65B PHE* 4.9 0.4 - + - -
66B GLY 5.9 0.4 - - - -
67B ASP* 4.1 4.2 + - - -
70B GLU* 3.6 22.0 - - - -
80B HIS* 4.7 4.9 - - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA 3.4 10.5 - - - +
40B MET* 3.7 11.9 - - + +
41B VAL 3.1 0.2 - - - -
42B TYR* 1.3 79.2 - - - +
44B GLY* 1.3 57.2 + - - +
45B ALA 3.8 1.2 + - - +
46B LYS* 5.9 0.5 - - - +
50B ARG* 4.5 6.8 + - - +
70B GLU* 3.6 25.7 - - + +
73B CYS* 5.5 3.6 - - - -
79B VAL* 6.3 0.7 - - + -
80B HIS* 3.2 26.7 - - + +
117B TYR* 4.2 11.7 - - + -
120B CYS* 4.5 16.6 - - + -
121B VAL* 5.4 1.3 - - + +
124B LEU* 4.3 16.6 - - + -
125B TYR* 3.8 31.9 - - + -
314B GLY* 5.3 0.7 - - - -
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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
------------------------------------------------------------
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