Contacts of the helix formed by residues 53 - 63 (chain A) in PDB entry 2YVX
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 PRO 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 3.2 21.5 - - - +
26A GLU* 4.2 15.5 - - + +
51A LEU 4.0 3.1 - - - +
52A LEU* 1.3 89.3 - - + +
54A LYS* 1.3 70.8 + - + +
55A ALA* 3.0 6.1 + - + +
56A LYS* 3.3 15.7 + - + +
57A ALA* 3.1 17.5 + - - +
80A ARG* 5.0 1.8 - - - +
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Residues in contact with LYS 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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52A LEU 3.8 0.8 + - - -
53A PRO* 1.3 72.1 - - + +
55A ALA* 1.3 65.6 + - - +
57A ALA* 3.8 2.9 + - - +
58A ALA* 3.2 20.6 + - - +
80A ARG* 4.6 6.8 - - - +
83A GLU* 2.9 44.1 + - + +
84A ILE* 4.9 5.1 - - - +
86A GLU* 6.2 2.1 - - - +
87A GLU* 3.6 36.9 + - + +
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Residues in contact with ALA 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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53A PRO* 3.0 5.3 + - + +
54A LYS* 1.3 77.5 - - - +
56A LYS* 1.3 66.2 + - + +
58A ALA* 2.9 15.4 + - - +
59A GLU* 3.0 15.3 + - - +
87A GLU* 3.4 27.3 + - + +
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Residues in contact with LYS 56 (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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25A LEU* 3.9 4.2 - - - +
26A GLU* 2.9 56.0 + - - +
27A GLU 4.4 0.2 - - - -
28A ILE* 3.0 26.3 + - + +
30A PRO* 4.2 24.7 - - + -
52A LEU* 3.5 18.2 - - + -
53A PRO* 3.3 22.7 + - + +
55A ALA* 1.3 79.9 - - + +
57A ALA* 1.3 63.4 + - - +
59A GLU* 3.3 2.6 + - - +
60A VAL* 3.0 28.8 + - - +
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Residues in contact with ALA 57 (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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49A LEU* 3.8 25.9 - - + +
52A LEU* 3.2 31.9 - - + +
53A PRO 3.1 14.8 + - - +
54A LYS* 4.0 4.0 - - - +
56A LYS* 1.3 80.5 - - - +
58A ALA* 1.3 63.1 + - - +
60A VAL* 3.7 1.7 + - - +
61A LEU* 3.4 19.6 + - - +
80A ARG* 5.2 4.0 - - - +
84A ILE* 4.5 14.4 - - + -
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Residues in contact with ALA 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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54A LYS 3.2 9.9 + - - +
55A ALA 2.9 10.0 + - - +
57A ALA* 1.3 76.4 - - - +
59A GLU* 1.3 69.1 + - - +
61A LEU* 3.2 9.4 + - - +
62A SER* 3.3 3.8 + - - -
84A ILE* 3.6 20.2 - - + +
87A GLU 3.3 26.7 - - - +
88A LEU* 3.2 31.6 - - + +
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Residues in contact with GLU 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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29A HIS* 6.1 2.2 - - + -
30A PRO* 4.6 17.0 - - + -
55A ALA 3.0 12.1 + - - +
56A LYS* 3.3 8.7 + - - +
58A ALA* 1.3 73.9 - - - +
60A VAL* 1.3 54.8 + - - +
61A LEU 2.8 13.5 + - - -
62A SER* 2.6 26.1 + - - -
63A HIS* 3.4 40.6 + - + +
88A LEU* 6.0 0.5 - - - +
89A SER* 5.5 8.8 + - - -
92A ASP* 5.1 3.8 - - - +
226B ASP* 4.6 5.9 - - - +
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Residues in contact with VAL 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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30A PRO* 3.4 34.3 - - + +
33A LEU* 3.9 24.2 - - + -
34A LEU* 3.5 30.6 - - + +
37A TRP* 4.8 9.9 - - + -
49A LEU* 5.8 4.9 - - + -
52A LEU* 4.2 12.6 - - + -
56A LYS 3.0 19.2 + - - +
57A ALA 4.0 4.7 - - - +
59A GLU* 1.3 73.5 - - - +
61A LEU* 1.3 59.1 + - - +
63A HIS 4.1 1.1 - - - -
64A LEU* 3.2 22.7 - - + +
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Residues in contact with LEU 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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49A LEU* 3.2 45.3 - - + -
57A ALA 3.4 7.1 + - - +
58A ALA* 3.2 10.9 + - - +
59A GLU 2.8 2.2 + - - -
60A VAL* 1.3 75.5 - - - +
62A SER* 1.3 58.5 + - - +
63A HIS 2.9 10.1 + - - -
64A LEU* 3.1 30.2 + - + +
69A GLN* 3.4 25.2 - - + +
72A TYR* 5.0 9.6 - - + +
73A LEU* 3.7 31.0 - - + -
76A LEU* 5.9 0.2 - - + -
84A ILE* 4.7 17.5 - - + -
85A LEU* 6.4 1.8 - - + -
88A LEU* 4.9 8.5 - - + -
96A ALA* 6.2 1.3 - - + -
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Residues in contact with SER 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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58A ALA 3.3 5.9 + - - -
59A GLU* 2.6 29.0 + - - -
61A LEU* 1.3 76.0 - - - +
63A HIS* 1.3 70.8 + - - +
64A LEU 3.3 3.8 + - - +
69A GLN* 4.1 18.3 + - - +
88A LEU* 4.4 8.4 - - - +
92A ASP* 3.2 41.3 + - - +
96A ALA* 5.4 0.7 - - - -
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Residues in contact with HIS 63 (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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31A GLN* 3.6 21.8 + - - +
34A LEU* 2.9 37.0 - - + +
59A GLU* 3.4 41.1 + - + +
61A LEU 2.9 1.6 + - - -
62A SER* 1.3 96.8 + - - +
64A LEU* 1.3 60.7 + - - +
92A ASP* 4.3 7.0 + - - -
224B ASP 4.2 7.8 + - - -
226B ASP* 3.9 21.1 + - + -
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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