Contacts of the helix formed by residues 45 - 59 (chain U) in PDB entry 7K63
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 GLY 45 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178I T 3.8 13.9 - - - -
179I A 5.1 1.3 - - - -
44U PRO* 1.3 76.4 - - - +
46U LYS* 1.3 67.6 + - - +
47U TYR 3.4 2.2 - - - -
48U SER* 3.8 16.2 - - - -
49U GLN* 2.9 26.7 + - - +
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Residues in contact with LYS 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I G 4.8 16.2 - - - +
178I T 3.6 9.4 + - - +
45U GLY* 1.3 71.3 - - - +
47U TYR* 1.3 66.9 + - + +
49U GLN* 3.9 4.8 - - - +
50U LEU* 2.9 27.2 + - - +
78U TRP* 3.4 57.4 - - + +
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Residues in contact with TYR 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I G 3.5 37.4 + - - -
178I T 3.1 10.4 + - - +
46U LYS* 1.3 85.3 - - + +
48U SER* 1.3 59.8 + - - +
50U LEU* 3.4 11.8 - - + +
51U VAL* 2.9 34.5 + - - +
78U TRP* 4.3 18.3 + + - -
79U PHE* 4.0 20.9 - + - -
80U ASP* 3.6 23.8 + - - +
84U GLY* 4.2 4.9 - - - -
87U TYR* 3.3 53.5 - + + +
88U LEU* 3.9 21.5 - - + -
91U SER* 3.7 2.9 - - - -
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Residues in contact with SER 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I T 3.3 20.0 + - - -
179I A 3.7 21.0 + - - -
44U PRO* 4.7 3.8 - - - -
45U GLY 3.8 16.8 + - - -
46U LYS 3.3 0.2 - - - -
47U TYR* 1.3 75.0 - - - +
49U GLN* 1.3 62.7 + - - +
51U VAL* 3.1 5.6 - - - +
52U VAL* 3.0 27.5 + - - +
91U SER* 3.0 19.2 + - - -
95U LEU* 4.2 14.1 - - - +
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Residues in contact with GLN 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U PRO* 3.4 38.8 - - + +
45U GLY 2.9 16.0 + - - +
46U LYS* 4.0 3.8 - - - +
48U SER* 1.3 76.0 - - - +
50U LEU* 1.3 63.6 + - - +
52U VAL* 3.8 6.1 - - + +
53U GLU* 2.9 37.9 + - - +
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Residues in contact with LEU 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U LYS 2.9 19.7 + - - +
47U TYR* 3.4 18.2 - - + +
48U SER 3.2 0.2 - - - -
49U GLN* 1.3 75.9 - - - +
51U VAL* 1.3 55.2 + - - +
53U GLU* 3.2 18.5 - - + +
54U THR* 2.5 48.5 + - - +
73U ALA* 4.2 17.9 - - + -
76U VAL* 3.6 35.7 - - + -
78U TRP* 4.1 20.6 - - + -
79U PHE* 4.3 16.6 - - + -
88U LEU* 4.6 4.5 - - + -
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Residues in contact with VAL 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U TYR 2.9 14.2 + - - +
48U SER 3.1 15.5 - - - +
50U LEU* 1.3 76.4 - - + +
52U VAL* 1.3 63.2 + - + +
54U THR* 3.8 6.2 - - - -
55U ILE* 3.0 34.7 + - + +
69U ILE* 4.3 17.3 - - + -
88U LEU* 3.6 33.0 - - + +
91U SER* 3.3 24.9 - - - +
92U ILE* 4.7 15.7 - - + -
95U LEU* 3.6 14.1 - - + -
101U LEU* 5.1 1.8 - - + -
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Residues in contact with VAL 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U SER 3.0 19.1 + - - +
49U GLN* 4.0 6.5 - - - +
51U VAL* 1.3 77.1 - - + +
53U GLU* 1.3 58.6 + - - +
55U ILE* 4.0 2.2 + - - +
56U ARG* 3.8 34.0 + - - +
95U LEU* 3.6 27.6 - - + -
100U THR* 5.1 8.7 - - + +
101U LEU* 5.0 8.5 - - + -
115U LEU* 4.2 23.1 - - + +
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Residues in contact with GLU 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U GLN* 2.9 34.1 + - - +
50U LEU* 3.2 24.6 + - + +
52U VAL* 1.3 78.8 - - - +
54U THR* 1.3 59.5 + - - +
55U ILE 3.2 0.4 - - - -
56U ARG* 3.3 13.0 + - - +
57U ARG* 2.9 29.0 + - - +
78U TRP* 4.9 8.1 - - - -
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Residues in contact with THR 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50U LEU* 2.5 39.6 + - - +
51U VAL* 3.8 7.2 - - - -
53U GLU* 1.3 75.3 - - - +
55U ILE* 1.3 60.9 + - - +
57U ARG* 3.3 12.3 + - - +
58U LEU* 2.9 56.4 + - + +
69U ILE* 4.1 20.4 - - + +
72U GLU* 4.2 11.2 - - + -
73U ALA* 4.6 5.0 - - - +
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Residues in contact with ILE 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U VAL* 3.0 21.5 + - + +
52U VAL* 4.2 4.5 - - - +
54U THR* 1.3 76.6 - - - +
56U ARG* 1.3 57.1 + - - +
58U LEU* 3.9 3.7 - - - +
59U GLY* 2.9 36.1 + - - +
64U SER* 4.9 5.8 + - - +
69U ILE* 4.0 26.9 - - + -
92U ILE* 5.3 0.4 - - + -
101U LEU* 3.5 36.8 - - + -
113U PHE* 4.1 24.7 - - + +
114U LYS* 4.3 1.8 - - - -
115U LEU* 3.9 26.7 - - + +
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Residues in contact with ARG 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U VAL* 3.8 22.3 + - - +
53U GLU* 3.3 13.7 + - - +
55U ILE* 1.3 81.6 - - - +
57U ARG* 1.3 61.4 + - - +
58U LEU 3.3 0.5 + - - -
59U GLY* 3.6 8.2 + - - -
115U LEU* 3.5 32.5 - - + +
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Residues in contact with ARG 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53U GLU 2.9 17.6 + - - +
54U THR* 3.8 11.0 + - - +
56U ARG* 1.3 76.5 - - - +
58U LEU* 1.3 72.2 + - - +
72U GLU* 2.7 61.0 + - - +
73U ALA* 5.2 0.2 - - - +
75U LYS* 4.3 10.3 - - - +
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Residues in contact with LEU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U THR* 2.9 36.7 + - + +
55U ILE 4.1 0.9 - - - +
57U ARG* 1.3 118.7 - - - +
59U GLY* 1.3 58.9 + - - +
60U GLU* 3.3 10.4 + - - +
64U SER* 3.8 9.6 - - - +
68U LYS* 3.2 37.4 + - - +
69U ILE* 4.1 9.4 - - + -
72U GLU* 3.6 22.2 - - + -
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Residues in contact with GLY 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55U ILE* 2.9 24.0 + - - +
56U ARG* 3.6 7.8 + - - -
58U LEU* 1.3 73.6 - - - +
60U GLU* 1.3 73.8 + - - +
61U ARG* 3.7 1.3 - - - -
63U GLY* 5.1 0.3 - - - -
64U SER* 4.2 3.2 + - - -
114U LYS* 5.8 1.4 - - - +
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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