Contacts of the helix formed by residues 67 - 80 (chain B) in PDB entry 3U44
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 SER 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.6 4.0 - - - -
39B VAL 3.4 13.5 - - - -
41B ASP* 3.7 36.0 + - - -
44B THR* 4.0 7.4 - - - +
66B PHE* 1.3 73.0 - - - +
68B PHE* 1.3 68.3 + - - +
69B SER* 3.0 7.3 + - - -
70B ARG* 3.5 27.2 + - - +
71B LEU* 2.9 23.2 + - - +
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Residues in contact with PHE 68 (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* 3.7 28.9 - - + +
41B ASP* 4.9 4.1 + - - +
67B SER* 1.3 73.4 - - - +
69B SER* 1.3 57.0 + - - +
71B LEU* 4.0 3.6 - - + +
72B ALA* 3.1 27.5 + - - +
187B LEU* 3.7 21.6 - - + +
190B LEU* 4.1 3.3 - - + +
210B PHE* 3.4 40.8 - + - -
213B PHE* 3.6 27.4 - + - -
217B GLU* 3.6 43.5 - - + +
220B VAL* 3.9 28.3 - - + -
221B LEU* 3.9 5.6 - - + -
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Residues in contact with SER 69 (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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41B ASP* 3.8 15.6 + - - -
67B SER* 3.0 8.8 - - - -
68B PHE* 1.3 75.7 - - - +
70B ARG* 1.3 56.7 + - - -
71B LEU 3.1 1.1 - - - -
72B ALA* 2.9 8.1 + - - +
73B TRP* 2.8 60.8 + - - +
186B TYR* 6.0 5.2 - - - -
187B LEU* 5.0 3.6 - - - +
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Residues in contact with ARG 70 (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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1013A LYS* 4.7 0.2 - - - +
1027A ASP* 3.3 45.7 + - - +
44B THR* 3.1 34.4 + - - +
48B GLU* 3.5 19.8 + - - -
65B VAL 3.0 27.2 + - - -
66B PHE* 3.8 13.0 - - + -
67B SER* 3.3 20.8 + - - +
69B SER* 1.3 78.9 - - - +
71B LEU* 1.3 56.9 + - - +
73B TRP* 3.6 25.9 - - + +
74B ARG* 2.9 36.9 + - + +
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Residues in contact with LEU 71 (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 ILE* 4.0 30.7 - - + -
38B LEU* 4.2 26.2 - - + -
66B PHE* 3.7 27.0 - - + -
67B SER 2.9 17.8 + - - +
68B PHE* 4.0 5.4 - - - +
70B ARG* 1.3 77.1 - - - +
72B ALA* 1.3 63.3 + - - +
74B ARG* 3.3 2.7 + - + +
75B VAL* 3.1 42.3 + - + +
190B LEU* 4.2 16.4 - - + -
194B ILE* 6.1 0.2 - - + -
200B ILE* 5.5 0.7 - - + -
220B VAL* 4.8 2.5 - - + -
224B LEU* 4.4 22.0 - - + -
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Residues in contact with ALA 72 (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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68B PHE 3.1 13.4 + - - +
69B SER* 2.9 10.4 + - - +
71B LEU* 1.3 79.1 - - - +
73B TRP* 1.3 63.3 + - - +
74B ARG 3.2 0.2 + - - -
75B VAL* 3.3 0.7 + - - -
76B LEU* 2.9 31.5 + - + +
186B TYR* 4.1 25.8 - - + +
187B LEU* 4.8 1.1 - - + -
190B LEU* 3.7 31.6 - - + +
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Residues in contact with TRP 73 (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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1027A ASP 5.7 6.5 - - - -
69B SER* 2.8 31.8 + - - +
70B ARG* 3.6 36.3 - - + +
72B ALA* 1.3 73.3 - - - +
74B ARG* 1.3 62.8 + - + +
76B LEU* 3.8 1.4 - - + +
77B GLN* 3.0 24.1 + - - +
82B MET* 3.4 38.0 - - + +
86B PHE* 6.6 0.2 - + - -
186B TYR* 3.0 41.0 + + - -
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Residues in contact with ARG 74 (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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1129A GLU* 3.8 13.7 + - - +
1131A PRO* 3.1 39.9 - - - +
1157A ILE* 3.7 20.4 - - - +
64B GLN* 3.5 12.0 + - - +
66B PHE* 3.2 26.1 - - + -
70B ARG* 2.9 27.3 + - + +
71B LEU* 3.5 5.4 - - + +
73B TRP* 1.3 75.0 - - + +
75B VAL* 1.3 67.1 + - + +
76B LEU 2.9 1.6 + - - -
77B GLN* 2.9 32.9 + - - +
78B HIS* 3.5 8.5 + - - +
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Residues in contact with VAL 75 (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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71B LEU* 3.1 27.9 + - + +
74B ARG* 1.3 80.5 - - + +
76B LEU* 1.3 57.3 + - + +
78B HIS* 3.5 5.6 + - - +
79B THR* 2.8 38.3 + - + +
190B LEU* 3.6 29.6 - - + -
193B HIS* 4.3 11.0 - - + +
194B ILE* 4.6 3.6 - - + +
197B ALA* 3.6 26.0 - - + -
199B ASP* 5.8 0.9 - - - +
200B ILE* 4.4 18.8 - - + -
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Residues in contact with LEU 76 (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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1094A LEU* 4.4 1.2 - - - +
72B ALA* 2.9 31.8 + - + +
73B TRP 3.8 1.3 - - - +
75B VAL* 1.3 75.8 - - - +
77B GLN* 1.3 58.4 + - - +
78B HIS 2.8 6.6 + - - -
79B THR* 3.6 3.6 - - - +
80B GLY* 2.7 37.7 + - - +
81B GLY 5.6 1.1 - - - -
82B MET* 3.6 28.9 - - + +
181B LEU* 6.2 0.2 - - + -
186B TYR* 4.5 19.7 - - + +
189B LEU* 4.2 33.2 - - + +
190B LEU* 4.5 3.6 - - - -
193B HIS* 3.3 39.0 - - + +
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Residues in contact with GLN 77 (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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1065A HIS* 6.1 0.8 + - - -
1066A THR* 5.5 10.3 + - + +
1070A HIS* 3.3 11.9 - - + -
1094A LEU* 3.1 19.7 - - - +
1129A GLU* 4.0 29.3 + - - +
73B TRP 3.0 12.6 + - - +
74B ARG* 2.9 26.5 + - - +
76B LEU* 1.3 74.5 - - - +
78B HIS* 1.3 56.9 + - - +
82B MET* 3.8 13.2 - - + +
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Residues in contact with HIS 78 (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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1069A GLN 5.1 7.2 - - - -
1070A HIS* 3.2 35.5 + + - -
1092A LYS* 5.3 4.2 + - - +
1094A LEU* 3.5 13.2 - - - +
74B ARG 3.5 5.4 + - - +
75B VAL* 3.6 9.6 - - - +
76B LEU 2.8 1.4 - - - -
77B GLN* 1.3 81.7 + - - +
79B THR* 1.3 66.0 + - + +
80B GLY 3.4 0.9 - - - -
197B ALA* 6.1 4.7 - - + -
198B GLU* 6.2 3.8 - - + -
199B ASP* 3.7 25.7 + - - -
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Residues in contact with THR 79 (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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1092A LYS* 4.0 20.1 - - - +
1094A LEU* 4.4 0.9 - - - -
75B VAL* 2.8 28.2 + - + +
76B LEU* 3.6 3.1 - - - +
78B HIS* 1.3 77.4 - - + +
80B GLY* 1.3 58.4 + - - +
193B HIS* 2.8 41.5 + - - +
196B LEU* 3.5 34.3 - - + +
197B ALA* 3.7 25.4 - - + -
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Residues in contact with GLY 80 (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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1092A LYS 3.2 13.5 - - - -
1094A LEU* 3.3 14.6 - - - -
76B LEU* 2.7 33.0 + - - +
78B HIS 3.4 0.6 - - - -
79B THR* 1.3 74.9 + - - +
81B GLY* 1.3 59.9 + - - -
82B MET 3.6 0.2 - - - -
189B LEU* 4.8 0.3 - - - +
193B HIS* 3.1 25.6 + - - -
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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