Contacts of the helix formed by residues 54 - 75 (chain S) in PDB entry 5L4K
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 LYS 54 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S GLU* 3.5 29.7 + - + +
53S GLY* 1.3 81.1 - - - +
55S THR* 1.3 61.8 + - - +
56S ALA 3.7 0.7 - - - -
57S ALA* 4.0 4.0 - - + +
58S ALA* 2.9 46.6 + - - +
61S GLU* 5.7 4.4 - - - +
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Residues in contact with THR 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S GLU* 3.3 15.0 + - - +
51S ALA* 3.7 15.1 + - - +
54S LYS* 1.3 78.6 - - - +
56S ALA* 1.3 61.9 + - - +
57S ALA 3.4 0.2 - - - -
58S ALA* 4.0 4.9 - - + +
59S ALA* 3.6 19.4 + - - +
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Residues in contact with ALA 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51S ALA 3.5 5.8 + - - +
52S ASP* 3.6 38.3 - - + +
55S THR* 1.3 75.5 - - - +
57S ALA* 1.3 61.2 + - - +
59S ALA* 4.1 6.1 - - - +
60S ALA* 3.7 18.5 + - - +
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Residues in contact with ALA 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S ASP 4.2 5.0 + - - +
53S GLY 3.6 24.9 - - - +
54S LYS* 4.0 5.7 - - + +
55S THR 3.4 0.2 - - - -
56S ALA* 1.3 78.1 - - - +
58S ALA* 1.3 58.9 + - - +
60S ALA* 3.5 6.4 + - - +
61S GLU* 3.0 32.0 + - + +
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Residues in contact with ALA 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S LYS* 2.9 43.0 + - - +
55S THR* 4.0 5.8 - - + +
56S ALA 3.5 0.2 - - - -
57S ALA* 1.3 75.5 - - - +
59S ALA* 1.3 60.2 + - - +
61S GLU* 3.2 10.8 + - - +
62S HIS* 2.9 38.4 + - + +
65S ARG* 4.3 2.0 + - - +
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Residues in contact with ALA 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S THR 3.6 16.5 + - - +
56S ALA* 4.4 6.1 - - - +
57S ALA 3.3 0.2 - - - -
58S ALA* 1.3 75.3 - - - +
60S ALA* 1.3 56.5 + - - +
61S GLU 3.0 4.3 - - - -
62S HIS* 3.0 14.9 + - + +
63S SER* 3.0 30.7 + - - -
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Residues in contact with ALA 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ALA 3.7 13.3 + - - +
57S ALA* 3.5 10.4 + - - +
59S ALA* 1.3 76.7 - - - +
61S GLU* 1.3 58.6 + - - +
63S SER* 4.4 6.1 - - - +
64S GLN* 2.9 14.8 + - - +
106S ARG 5.4 3.4 - - - +
107S ARG* 2.9 32.3 - - - +
109S ASN* 5.5 8.1 - - - +
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Residues in contact with GLU 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54S LYS* 5.7 4.5 - - - +
57S ALA* 3.0 19.3 + - + +
58S ALA* 3.3 13.5 - - - +
59S ALA 3.0 0.2 - - - -
60S ALA* 1.3 77.6 - - - +
62S HIS* 1.3 59.7 + - - +
63S SER 3.3 0.2 - - - -
64S GLN* 2.6 44.6 + - - +
65S ARG* 2.9 66.0 + - - +
112S VAL* 4.0 19.1 - - - +
113S LEU* 4.8 2.6 - - - +
141S THR* 4.8 6.6 + - - +
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Residues in contact with HIS 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S ALA* 2.9 35.5 + - + +
59S ALA* 3.0 11.2 + - + +
61S GLU* 1.3 75.9 - - - +
63S SER* 1.3 58.4 + - - +
65S ARG* 3.5 21.4 + - - +
66S GLU* 2.9 28.1 + - - +
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Residues in contact with SER 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59S ALA 3.0 15.3 + - - -
60S ALA* 4.2 5.0 - - - -
62S HIS* 1.3 75.5 - - - +
64S GLN* 1.3 60.2 + - - +
66S GLU* 3.2 11.2 + - - +
67S LEU* 2.9 28.9 + - - +
107S ARG* 3.5 36.4 - - - +
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Residues in contact with GLN 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ALA 2.9 21.5 + - - +
61S GLU* 2.6 43.0 + - - +
62S HIS 3.5 0.2 - - - -
63S SER* 1.3 75.0 - - - +
65S ARG* 1.3 57.6 + - + +
67S LEU* 3.1 18.5 + - - +
68S ASP* 3.1 19.3 + - - +
107S ARG 3.3 13.9 + - - +
108S LEU* 3.7 14.5 - - + +
109S ASN* 4.8 5.9 + - - -
111S TYR* 3.0 42.8 - - + +
112S VAL* 3.7 3.0 + - - +
113S LEU* 3.9 28.7 - - + +
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Residues in contact with ARG 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S ALA* 4.3 3.4 + - - +
61S GLU* 2.9 57.9 + - - +
62S HIS* 3.7 27.0 + - - +
64S GLN* 1.3 79.2 - - - +
66S GLU* 1.3 58.1 + - - +
68S ASP* 4.1 11.7 - - - +
69S THR* 3.2 19.6 + - - -
113S LEU* 3.9 26.2 - - + -
141S THR* 4.7 12.1 + - - +
143S ALA* 4.5 13.2 - - + +
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Residues in contact with GLU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62S HIS 2.9 17.0 + - - +
63S SER* 3.6 9.5 - - - +
64S GLN 3.2 0.8 - - - -
65S ARG* 1.3 76.8 - - - +
67S LEU* 1.3 64.8 + - - +
68S ASP 3.2 0.2 - - - -
69S THR* 3.0 11.1 + - - -
70S VAL* 3.0 26.3 + - + +
107S ARG* 4.1 15.5 + - - +
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Residues in contact with LEU 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S SER 2.9 13.7 + - - +
64S GLN 3.5 7.6 - - - +
66S GLU* 1.3 73.9 - - - +
68S ASP* 1.3 71.3 + - - +
70S VAL* 2.9 14.4 + - + +
71S THR* 2.9 32.5 + - + +
101S LEU* 4.9 7.6 - - + +
104S THR* 3.4 26.2 - - - +
105S SER* 4.1 6.1 - - - -
107S ARG* 3.4 24.6 - - - +
108S LEU* 3.6 42.0 - - + -
111S TYR* 5.4 3.6 - - + +
170S LEU* 6.2 2.7 - - + -
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Residues in contact with ASP 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S GLN* 3.1 16.4 + - - +
65S ARG* 4.1 11.4 - - - +
66S GLU 3.2 0.2 - - - -
67S LEU* 1.3 77.2 - - - +
69S THR* 1.3 57.0 + - - +
71S THR* 3.2 12.0 + - - -
72S LEU* 3.0 33.1 + - - +
108S LEU* 4.2 3.6 - - - +
111S TYR* 3.5 29.4 + - - -
113S LEU* 4.5 11.3 - - - +
117S VAL* 3.5 24.9 - - - +
145S LEU* 3.6 24.7 - - + +
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Residues in contact with THR 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65S ARG 3.2 14.9 + - - -
66S GLU* 3.0 13.7 + - - -
68S ASP* 1.3 78.9 - - - +
70S VAL* 1.3 58.9 + - - +
72S LEU* 3.6 21.0 + - + +
73S GLU* 2.7 36.7 - - - +
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Residues in contact with VAL 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66S GLU* 3.0 24.0 + - + +
67S LEU* 2.9 13.9 + - + +
69S THR* 1.3 75.0 - - - +
71S THR* 1.3 62.5 + - + +
72S LEU 3.1 1.8 - - - -
73S GLU* 2.9 21.9 + - + +
74S ASP* 2.9 27.0 + - - +
101S LEU* 4.2 20.6 - - + -
107S ARG* 4.5 10.5 - - - +
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Residues in contact with THR 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S LEU* 2.9 31.1 + - + +
68S ASP* 3.2 15.4 + - - -
70S VAL* 1.3 74.7 - - + +
72S LEU* 1.3 57.3 + - - +
73S GLU 3.2 0.2 - - - -
74S ASP* 3.7 11.0 - - - +
75S ILE* 3.1 44.8 + - - +
101S LEU* 5.0 7.2 - - + -
111S TYR* 5.6 1.2 + - - -
117S VAL* 5.9 2.9 - - - +
121S PHE* 4.7 7.1 - - - -
145S LEU* 5.8 2.4 - - - +
166S TYR* 4.1 19.7 - - + +
167S LEU* 5.4 5.2 - - + +
170S LEU* 5.3 8.7 - - + -
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Residues in contact with LEU 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S ASP 3.0 18.2 + - - +
69S THR* 3.6 23.3 - - + +
70S VAL 3.1 0.4 - - - -
71S THR* 1.3 78.6 - - - +
73S GLU* 1.3 66.5 + - - +
75S ILE* 5.2 0.2 - - - -
76S LYS* 2.8 58.6 + - + +
77S GLU 3.8 0.3 + - - -
121S PHE* 5.1 5.8 - - + -
145S LEU* 4.3 31.0 - - + -
146S GLN* 4.5 16.6 - - + +
147S PHE* 4.1 23.6 - - + -
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Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S THR* 2.7 33.2 - - - +
70S VAL* 2.9 10.6 + - - +
72S LEU* 1.3 85.8 - - - +
74S ASP* 1.3 63.6 + - - +
75S ILE 3.3 1.3 - - - -
76S LYS* 4.1 9.4 + - - -
77S GLU* 3.6 23.8 - - + +
78S HIS* 2.8 36.7 + - + +
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Residues in contact with ASP 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70S VAL* 2.9 35.6 + - - +
71S THR* 3.6 6.2 + - - -
73S GLU* 1.3 79.2 - - - +
75S ILE* 1.3 59.4 + - - +
78S HIS* 3.5 2.7 - - - +
79S VAL* 3.2 13.1 + - - +
94S VAL* 3.6 24.8 - - - +
95S LEU* 3.1 29.2 - - + +
97S ALA* 4.3 7.7 - - - +
101S LEU* 3.6 12.8 - - - +
166S TYR* 3.3 30.1 + - + +
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Residues in contact with ILE 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S THR* 3.1 17.2 + - - +
74S ASP* 1.3 80.5 - - - +
76S LYS* 1.3 68.5 + - - +
77S GLU 3.3 1.3 - - - -
79S VAL* 3.3 12.4 + - + +
80S LYS* 3.2 24.3 + - - +
121S PHE* 3.5 39.9 - - + -
147S PHE* 5.9 0.9 - - + -
163S VAL* 3.4 35.9 - - + -
166S TYR* 3.8 35.4 - - + -
167S LEU* 4.1 7.0 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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