Contacts of the helix formed by residues 45 - 64 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.4 1.2 - - - +
44A ALA* 1.3 80.8 - - + +
46A VAL* 1.3 64.2 + - - +
47A GLN* 2.7 41.9 + - - +
48A ASP* 3.0 22.7 + - - +
49A GLN* 2.9 26.6 + - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.7 2.6 + - - -
45A ASP* 1.3 77.5 + - - +
47A GLN* 1.3 60.7 + - - +
49A GLN* 3.7 4.0 - - + +
50A ALA* 2.9 29.2 + - - +
83A ASP* 3.7 34.8 - - + +
86A THR* 4.0 21.3 - - + +
87A ILE* 4.0 17.0 - - + -
118A LYS* 3.7 37.0 - - + +
119A LEU* 5.6 1.1 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 2.7 21.0 + - - +
46A VAL* 1.3 76.1 - - - +
48A ASP* 1.3 63.8 + - - +
50A ALA* 3.4 2.6 + - - +
51A ARG* 3.0 28.8 + - - +
86A THR* 3.9 19.7 - - + +
90A VAL* 3.6 25.0 - - + +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.7 23.3 - - + +
45A ASP* 3.0 25.6 + - - +
47A GLN* 1.3 81.2 - - - +
49A GLN* 1.3 66.3 + - - +
51A ARG* 3.4 6.5 + - - +
52A LEU* 3.0 25.1 + - - +
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Residues in contact with GLN 49 (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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34A PRO* 3.3 31.2 - - + +
42A ILE* 3.7 11.5 - - - +
43A PRO* 2.9 33.0 + - + +
44A ALA* 3.8 12.3 + - - +
45A ASP 2.9 11.9 + - - +
46A VAL* 3.7 8.1 - - + +
48A ASP* 1.3 77.9 - - - +
50A ALA* 1.3 62.5 + - - +
52A LEU 3.3 0.2 + - - -
53A SER* 2.9 29.3 + - - -
116A ASP 5.3 1.4 + - - -
117A VAL* 3.8 1.6 - - - +
118A LYS* 2.8 50.3 + - + +
119A LEU* 3.8 7.1 - - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL 2.9 17.1 + - - +
47A GLN* 3.7 4.5 - - - +
49A GLN* 1.3 76.3 - - - +
51A ARG* 1.3 63.9 + - - +
53A SER* 3.5 2.1 + - - -
54A LEU* 3.2 29.2 + - + +
87A ILE* 4.2 20.6 - - + +
90A VAL* 4.0 22.2 - - + -
119A LEU* 3.9 23.6 - - + +
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Residues in contact with ARG 51 (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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47A GLN* 3.0 17.1 + - + +
48A ASP* 3.8 8.3 - - - +
49A GLN 3.3 0.2 - - - -
50A ALA* 1.3 77.2 - - - +
52A LEU* 1.3 57.2 + - - +
54A LEU* 3.3 5.1 + - - +
55A GLU* 2.9 65.5 + - + +
58A LYS* 5.6 1.2 - - - +
90A VAL* 3.6 18.9 + - + +
93A GLN* 4.9 1.8 - - - +
94A PHE* 3.9 29.0 - - - +
97A GLU* 3.1 36.2 + - - -
98A HIS* 4.9 3.6 - - - -
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Residues in contact with LEU 52 (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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34A PRO* 3.5 30.7 - - + -
35A VAL 4.1 2.5 - - - +
36A OCS 3.7 33.0 - - + +
37A PRO* 4.2 7.9 - - + -
43A PRO* 3.6 23.1 - - + -
48A ASP 3.0 17.1 + - - +
49A GLN 3.8 3.1 - - - +
51A ARG* 1.3 73.9 - - - +
53A SER* 1.3 68.1 + - - +
55A GLU* 3.2 10.9 + - + +
56A ASN* 3.0 36.9 + - - +
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Residues in contact with SER 53 (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 GLN* 3.8 16.4 + - - +
33A ILE 3.7 10.0 - - - -
34A PRO* 3.3 24.5 - - - +
49A GLN 2.9 16.9 + - - -
50A ALA 3.8 3.8 - - - -
52A LEU* 1.3 75.1 - - - +
54A LEU* 1.3 63.0 + - - +
56A ASN* 3.2 5.1 + - - +
57A VAL* 3.0 26.7 + - - +
119A LEU* 3.4 11.2 - - - +
121A ILE* 4.0 17.0 - - - -
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Residues in contact with LEU 54 (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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50A ALA* 3.2 20.2 + - + +
51A ARG* 3.7 4.5 - - - +
53A SER* 1.3 77.7 - - - +
55A GLU* 1.3 59.9 + - - +
57A VAL* 3.2 8.6 + - + +
58A LYS* 2.9 27.7 + - - +
74A MET* 4.5 13.7 - - + -
87A ILE* 5.5 1.1 - - + +
90A VAL* 4.0 11.4 - - + -
91A TYR* 3.8 42.8 - - + +
94A PHE* 3.6 46.7 - - + -
121A ILE* 3.7 24.9 - - + -
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Residues in contact with GLU 55 (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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9A ARG 4.9 0.8 - - - +
51A ARG* 2.9 59.6 + - + +
52A LEU* 3.2 15.7 + - + +
54A LEU* 1.3 76.1 - - - +
56A ASN* 1.3 60.0 + - - +
58A LYS* 2.7 38.5 + - - +
59A ALA* 2.9 28.6 + - - +
94A PHE* 3.6 18.2 - - - -
98A HIS* 4.8 0.5 - - - -
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Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG 4.0 3.1 - - - +
10A ALA* 3.8 8.1 - - + +
11A PRO* 3.3 23.9 - - + +
32A GLN* 3.6 20.4 + - + +
33A ILE 3.0 25.7 + - - -
35A VAL 3.1 19.2 + - - +
37A PRO* 3.9 14.0 - - - +
52A LEU* 3.0 21.2 + - - +
53A SER 3.5 8.1 - - - +
54A LEU 3.2 0.2 - - - -
55A GLU* 1.3 76.0 - - - +
57A VAL* 1.3 65.4 + - - +
59A ALA* 3.4 10.0 + - - +
60A ILE* 3.4 19.9 + - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 4.6 5.6 - - + +
32A GLN* 3.6 23.1 - - + -
53A SER 3.0 14.7 + - - +
54A LEU* 3.2 11.9 + - + +
56A ASN* 1.3 75.8 - - - +
58A LYS* 1.3 63.0 + - - +
60A ILE* 3.2 7.0 + - - +
61A VAL* 3.1 24.2 + - + +
71A ILE* 3.9 18.2 - - + -
74A MET* 4.3 4.0 - - + -
94A PHE* 5.6 2.0 - - + -
121A ILE* 3.7 27.1 - - + +
123A ALA* 3.6 28.5 - - + -
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Residues in contact with LYS 58 (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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51A ARG* 5.6 0.8 - - - +
54A LEU 2.9 13.8 + - - +
55A GLU* 2.7 40.8 + - - +
56A ASN 3.3 0.4 - - - -
57A VAL* 1.3 76.0 - - - +
59A ALA* 1.3 60.7 + - - +
61A VAL* 3.3 4.5 + - - +
62A VAL* 2.9 50.1 + - + +
68A VAL* 3.8 18.2 - - + -
94A PHE* 4.0 10.3 - - + -
98A HIS* 3.8 29.7 + - + +
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Residues in contact with ALA 59 (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 THR* 3.8 5.3 + - + +
9A ARG* 3.4 47.0 - - + +
10A ALA* 4.0 4.3 - - + +
55A GLU 2.9 14.7 + - - +
56A ASN 3.6 6.1 - - - +
57A VAL 3.2 0.4 - - - -
58A LYS* 1.3 79.7 - - - +
60A ILE* 1.3 58.8 + - - +
62A VAL* 3.6 5.7 + - - +
63A ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 60 (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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5A ILE* 3.6 22.7 - - + +
7A THR* 4.2 7.2 - - + -
10A ALA* 3.9 14.4 - - + -
19A GLN* 3.6 35.0 - - + +
20A GLY* 4.0 6.7 - - - -
27A VAL* 5.3 0.2 - - + -
29A THR* 3.9 18.6 - - + -
32A GLN* 3.2 44.6 - - + +
56A ASN 3.4 9.2 - - - +
57A VAL* 3.2 6.6 + - - +
59A ALA* 1.3 76.3 - - - +
61A VAL* 1.3 65.6 + - - +
63A ALA* 3.2 4.9 + - - +
64A ALA* 3.2 19.6 + - - +
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Residues in contact with VAL 61 (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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27A VAL* 5.2 5.6 - - + -
29A THR* 4.1 20.0 - - + -
57A VAL* 3.1 17.9 + - + +
58A LYS* 3.9 5.8 - - - +
60A ILE* 1.3 74.1 - - - +
62A VAL* 1.3 60.3 + - - +
64A ALA* 3.2 11.5 + - - +
66A LEU* 3.0 38.5 + - + +
67A SER 3.3 32.3 - - - +
68A VAL 4.4 0.9 - - - +
71A ILE* 4.2 23.6 - - + -
123A ALA* 4.9 1.3 - - + -
125A ALA* 4.5 16.2 - - + -
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Residues in contact with VAL 62 (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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9A ARG* 5.2 12.6 - - - +
58A LYS* 2.9 39.8 + - + +
59A ALA* 3.9 5.6 - - - +
61A VAL* 1.3 78.3 - - + +
63A ALA* 1.3 57.0 + - - +
65A GLY* 2.9 20.6 + - - -
66A LEU 3.3 16.9 - - - +
67A SER* 4.6 9.2 - - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.6 19.8 - - + +
6A GLU 4.6 3.8 - - - +
7A THR* 3.8 21.8 - - + +
59A ALA 2.9 18.9 + - - +
60A ILE 3.2 6.2 + - - +
62A VAL* 1.3 76.7 - - - +
64A ALA* 1.3 60.1 + - - +
65A GLY 3.2 1.0 + - - -
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Residues in contact with ALA 64 (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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5A ILE* 3.5 33.4 - - + +
22A ASP* 3.8 7.9 - - - +
27A VAL* 3.9 20.9 - - + -
60A ILE 3.2 5.8 + - - +
61A VAL* 3.5 11.0 - - - +
62A VAL 3.1 1.2 - - - -
63A ALA* 1.3 75.9 - - - +
65A GLY* 1.3 55.9 + - - +
66A LEU* 4.7 1.8 - - + +
127A ARG* 2.7 29.7 + - - +
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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