Contacts of the helix formed by residues 45 - 64 (chain B) in PDB entry 2UYK
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 ASP 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 3.4 1.2 - - - +
44B ALA* 1.3 78.1 - - - +
46B VAL* 1.3 61.8 + - - +
47B GLN* 2.8 47.5 + - - +
48B ASP* 3.1 24.0 + - - +
49B GLN* 2.9 27.4 + - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 3.6 3.2 + - - -
45B ASP* 1.3 76.7 + - - +
47B GLN* 1.3 60.4 + - + +
49B GLN* 4.2 4.7 - - + -
50B ALA* 2.9 29.3 + - - +
83B ASP* 3.8 26.2 - - + +
86B THR* 3.7 26.2 - - + -
87B ILE* 3.8 25.8 - - + -
118B LYS* 3.7 35.7 - - + +
119B LEU* 5.3 1.8 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 2.8 25.2 + - - +
46B VAL* 1.3 77.2 - - - +
48B ASP* 1.3 64.4 + - - +
50B ALA* 3.5 2.3 + - - +
51B ARG* 3.1 23.2 + - - +
86B THR* 3.5 24.8 - - + +
90B VAL* 4.0 23.8 - - + +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 3.7 24.6 - - + +
45B ASP* 3.1 26.6 + - + +
47B GLN* 1.3 80.4 - - - +
49B GLN* 1.3 66.1 + - - +
51B ARG* 3.4 5.2 + - - +
52B LEU* 3.0 25.3 + - - +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PRO* 3.3 30.5 - - + +
42B ILE* 3.6 11.5 - - + +
43B PRO* 2.9 32.3 + - + +
44B ALA* 3.7 12.1 + - - +
45B ASP 2.9 11.7 + - - +
46B VAL* 3.3 8.5 + - + +
48B ASP* 1.3 77.9 - - - +
50B ALA* 1.3 62.3 + - - +
52B LEU 3.3 0.3 + - - -
53B SER* 2.9 29.5 + - - -
116B ASP 5.3 1.2 + - - -
117B VAL* 4.7 1.6 - - - +
118B LYS* 2.8 51.0 + - - +
119B LEU* 3.7 8.5 + - + -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL 2.9 16.6 + - - +
47B GLN 3.8 5.2 - - - +
48B ASP 3.3 0.2 - - - -
49B GLN* 1.3 76.5 - - - +
51B ARG* 1.3 62.6 + - - +
53B SER* 3.5 2.1 + - - -
54B LEU* 3.1 30.8 + - + +
87B ILE* 4.3 19.1 - - + +
90B VAL* 3.9 21.5 - - + -
119B LEU* 3.9 23.0 - - + +
121B ILE* 4.7 0.7 - - + +
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Residues in contact with ARG 51 (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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47B GLN 3.1 14.6 + - - +
48B ASP* 3.9 5.4 - - - +
50B ALA* 1.3 80.4 - - - +
52B LEU* 1.3 58.3 + - - +
54B LEU* 3.3 3.9 + - - +
55B GLU* 2.9 56.2 + - + +
90B VAL* 3.7 17.3 + - + +
93B GLN* 5.8 1.4 - - - +
94B PHE* 3.7 33.8 - - - +
97B GLU* 3.4 28.3 + - - -
98B HIS* 5.0 4.8 - - - -
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Residues in contact with LEU 52 (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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34B PRO* 3.5 31.2 - - + +
35B VAL 4.0 7.9 - - - +
36B OCS 3.7 35.7 - - + +
37B PRO* 4.2 2.9 - - + -
43B PRO* 3.6 21.1 - - + -
48B ASP 3.0 17.1 + - - +
49B GLN 3.9 2.7 - - - +
51B ARG* 1.3 75.1 - - - +
53B SER* 1.3 60.8 + - - +
55B GLU* 3.2 11.1 + - + -
56B ASN* 2.8 47.2 + - - +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 3.6 18.3 + - - +
33B ILE 4.5 4.0 - - - -
34B PRO* 3.4 24.7 - - - +
49B GLN 2.9 19.7 + - - -
50B ALA 3.9 4.0 - - - -
52B LEU* 1.3 75.4 - - - +
54B LEU* 1.3 58.3 + - - +
56B ASN* 3.3 6.7 + - - +
57B VAL* 3.0 32.8 + - - +
119B LEU* 3.6 8.6 - - - +
121B ILE* 3.9 20.0 - - - -
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Residues in contact with LEU 54 (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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50B ALA* 3.1 21.3 + - + +
51B ARG* 3.6 7.0 - - - +
53B SER* 1.3 77.4 - - - +
55B GLU* 1.3 55.2 + - - +
57B VAL* 3.2 6.2 + - + +
58B LYS* 2.8 29.6 + - - +
74B MET* 4.2 20.6 - - + -
90B VAL* 4.4 3.8 - - + +
91B TYR* 3.8 44.9 - - + +
94B PHE* 3.8 46.6 - - + -
95B PHE* 4.5 1.6 - - + -
121B ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 4.8 4.7 + - - +
51B ARG* 2.9 60.8 + - + +
52B LEU* 3.2 14.6 + - + +
54B LEU* 1.3 74.6 - - - +
56B ASN* 1.3 58.2 + - - +
58B LYS* 3.4 23.1 + - - +
59B ALA* 2.9 30.2 + - - +
94B PHE* 3.6 11.4 - - + -
98B HIS* 5.0 0.2 - - - -
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Residues in contact with ASN 56 (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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9B ARG 4.0 2.8 - - - +
10B ALA* 3.8 10.7 - - + +
11B PRO* 3.3 24.2 - - + +
32B GLN* 3.6 20.1 + - + +
33B ILE 3.0 25.9 + - - -
35B VAL 3.1 18.6 + - - +
37B PRO* 3.9 12.5 - - - +
52B LEU* 2.8 24.9 + - - +
53B SER 3.6 4.7 - - - +
55B GLU* 1.3 75.4 - - - +
57B VAL* 1.3 66.9 + - - +
59B ALA* 3.3 10.8 + - - +
60B ILE* 3.4 18.5 + - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 4.5 6.9 - - + +
32B GLN* 3.6 21.0 - - + +
53B SER 3.0 19.2 + - - +
54B LEU* 3.2 8.9 + - + +
56B ASN* 1.3 75.1 - - - +
58B LYS* 1.3 64.8 + - - +
60B ILE* 3.1 7.8 + - - +
61B VAL* 3.0 23.1 + - + +
71B ILE* 4.1 12.8 - - + -
74B MET* 3.8 11.4 - - + -
94B PHE* 6.5 0.4 - - + -
121B ILE* 3.6 30.7 - - + +
123B ALA* 3.6 26.9 - - + -
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Residues in contact with LYS 58 (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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54B LEU 2.8 19.7 + - - +
55B GLU* 3.5 24.5 + - - +
57B VAL* 1.3 75.9 - - - +
59B ALA* 1.3 57.4 + - - +
61B VAL* 3.2 6.6 + - - +
62B VAL* 2.8 50.8 + - + +
68B VAL* 3.6 17.5 - - + -
71B ILE* 5.5 1.6 - - - -
94B PHE* 4.0 12.8 - - + -
98B HIS* 2.7 40.1 + - + +
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Residues in contact with ALA 59 (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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7B THR* 3.9 6.0 + - + +
9B ARG* 3.3 48.9 - - + +
10B ALA* 3.9 3.4 - - + +
55B GLU 2.9 15.1 + - - +
56B ASN 3.6 6.1 - - - +
57B VAL 3.2 0.2 - - - -
58B LYS* 1.3 76.9 - - - +
60B ILE* 1.3 56.1 + - - +
62B VAL* 3.9 5.0 - - - +
63B ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 60 (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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5B ILE* 3.6 24.8 - - + +
7B THR* 4.1 9.0 - - + -
10B ALA* 4.1 11.4 - - + -
19B GLN* 3.6 35.4 - - + +
20B GLY* 4.0 8.5 - - - -
27B VAL* 5.2 0.2 - - + -
29B THR* 3.8 20.6 - - + -
32B GLN* 3.3 42.2 - - + +
56B ASN 3.4 10.5 + - - +
57B VAL* 3.1 7.0 + - - +
59B ALA* 1.3 75.9 - - - +
61B VAL* 1.3 64.4 + - - +
63B ALA* 3.3 1.9 + - - -
64B ALA* 3.2 19.1 + - - +
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Residues in contact with VAL 61 (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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27B VAL* 4.9 5.6 - - + -
29B THR* 4.1 17.9 - - + -
57B VAL* 3.0 18.6 + - + +
58B LYS* 3.8 8.5 - - - +
60B ILE* 1.3 74.5 - - - +
62B VAL* 1.3 61.0 + - - +
64B ALA* 3.2 14.1 + - - +
66B LEU* 3.1 39.4 + - + +
67B SER 3.5 28.9 - - - +
68B VAL 5.5 0.2 - - - +
71B ILE* 4.2 19.3 - - + -
123B ALA* 5.1 2.0 - - + -
125B ALA* 4.2 17.5 - - + -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS* 2.8 45.8 + - + +
59B ALA* 3.9 5.4 - - - +
61B VAL* 1.3 75.0 - - + +
63B ALA* 1.3 59.0 + - - +
65B GLY* 2.8 21.3 + - - -
66B LEU 3.4 16.2 - - - +
67B SER* 4.9 6.5 - - - -
68B VAL 5.4 0.4 - - - +
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Residues in contact with ALA 63 (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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5B ILE* 3.6 19.1 - - + +
6B GLU 4.3 4.9 - - - +
7B THR* 3.8 20.6 - - - +
59B ALA 2.9 19.1 + - - +
60B ILE 3.3 6.0 + - - +
62B VAL* 1.3 76.9 - - - +
64B ALA* 1.3 58.5 + - - +
65B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 64 (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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5B ILE* 3.6 31.6 - - + +
22B ASP* 3.9 9.9 - - - +
27B VAL* 3.8 21.3 - - + -
60B ILE 3.2 6.9 + - - +
61B VAL 3.5 10.8 - - - +
62B VAL 3.1 1.0 - - - -
63B ALA* 1.3 77.2 - - - +
65B GLY* 1.3 54.8 + - - +
66B LEU* 3.4 1.8 - - + +
127B ARG* 2.8 28.3 + - - +
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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
------------------------------------------------------------
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