Contacts of the helix formed by residues 99 - 115 (chain I) in PDB entry 5KZ5
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 ALA 99 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ARG* 3.4 25.7 - - - +
97I ARG 3.5 1.2 - - - -
98I LEU* 1.3 76.3 - - - +
100I GLU* 1.3 64.7 + - + +
102I THR* 3.6 8.2 + - - -
103I LEU* 3.5 23.2 + - - +
147I LYS* 5.6 6.1 - - + -
152I LYS* 4.1 26.2 - - + +
154I ILE* 5.0 10.9 - - + +
168I TRP* 3.9 13.4 - - + +
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Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ARG* 5.3 2.2 - - - +
97I ARG* 3.5 35.8 + - + +
98I LEU 3.4 0.2 - - - -
99I ALA* 1.3 77.3 - - + +
101I GLU* 1.4 61.2 + - - +
103I LEU* 3.5 13.0 + - - +
104I ASP* 3.2 21.0 + - - +
147I LYS* 3.3 36.4 + - + +
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Residues in contact with GLU 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I GLU* 3.2 25.1 + - - +
97I ARG* 3.3 43.1 + - - +
98I LEU* 3.3 14.9 + - - +
100I GLU* 1.4 76.7 - - - +
102I THR* 1.4 57.9 + - - +
104I ASP* 3.3 5.6 + - + +
105I SER* 2.9 31.4 + - - -
205I TYR* 3.2 34.7 + - + +
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Residues in contact with THR 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I LEU* 2.9 28.2 + - - +
99I ALA* 3.9 6.5 - - - -
101I GLU* 1.4 70.3 - - - +
103I LEU* 1.4 62.4 + - + +
105I SER* 3.0 19.1 + - - -
106I LEU* 3.1 23.0 + - + +
173I TRP* 3.2 57.1 - - + +
182I LEU* 5.5 5.6 - - + -
183I HIS* 5.3 2.2 - - + -
203I LEU* 4.1 8.9 - - + +
205I TYR* 4.3 9.7 - - - -
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Residues in contact with LEU 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I ALA 3.5 16.6 - - - +
100I GLU* 3.5 11.4 + - - +
101I GLU 3.3 0.4 - - - -
102I THR* 1.4 79.6 - - + +
104I ASP* 1.4 61.5 + - - +
106I LEU* 3.5 16.9 - - + +
107I ALA* 3.3 21.1 + - - +
129I SER 5.6 2.2 - - - +
145I ILE* 6.0 1.1 - - + -
147I LYS* 4.7 16.4 - - + -
154I ILE* 4.1 30.3 - - + -
182I LEU* 5.2 7.9 - - + -
91S ARG* 3.6 51.4 - - - +
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Residues in contact with ASP 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I ARG* 5.0 10.3 + - - +
100I GLU 3.2 11.2 + - - +
101I GLU* 3.5 12.7 - - + +
103I LEU* 1.4 75.3 - - - +
105I SER* 1.4 64.5 + - - +
107I ALA* 3.4 8.4 + - - +
108I GLU* 3.1 28.8 + - - +
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Residues in contact with SER 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I GLU* 2.9 16.6 + - - -
102I THR* 3.0 22.5 + - - -
104I ASP* 1.4 73.4 + - - +
106I LEU* 1.3 57.9 + - - +
108I GLU* 3.1 6.5 + - - +
109I PHE* 2.9 55.8 + - - -
203I LEU* 3.5 10.1 - - - +
205I TYR* 3.7 19.0 - - - -
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Residues in contact with LEU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I THR* 3.1 23.2 + - + +
103I LEU* 3.5 19.3 - - + +
104I ASP 3.3 0.2 - - - -
105I SER* 1.3 75.6 + - - +
107I ALA* 1.3 64.8 + - - +
109I PHE* 4.2 3.0 - - - +
110I PHE* 3.4 22.1 + - + +
182I LEU* 5.1 5.8 - - + -
183I HIS* 3.7 31.9 - - + +
186I LEU* 4.8 14.1 - - + -
200I LEU* 3.9 30.0 - - + +
202I SER 5.5 0.4 - - - -
203I LEU* 4.0 10.8 - - + -
91S ARG* 6.6 0.2 - - + -
92S THR* 4.8 20.4 - - + +
93S HIS 5.9 0.2 - - - +
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Residues in contact with ALA 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I LEU 3.3 10.1 + - - +
104I ASP* 3.5 11.2 - - - +
105I SER 3.3 0.4 - - - -
106I LEU* 1.3 82.7 - - - +
108I GLU* 1.4 57.3 + - - +
110I PHE* 3.4 4.4 + - - +
111I GLU* 3.1 34.3 + - - +
91S ARG* 4.0 9.9 - - - +
92S THR* 3.8 17.9 - - - +
93S HIS* 3.6 22.7 + - + +
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Residues in contact with GLU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ASP* 3.1 22.7 + - - +
105I SER* 3.1 9.4 + - - +
107I ALA* 1.4 72.6 - - - +
109I PHE* 1.4 66.3 + - + +
111I GLU* 3.3 25.4 + - - +
112I ASP* 3.0 25.9 + - - +
85P TYR* 5.0 11.2 - - + -
294P GLY* 3.5 3.2 - - - -
295P THR* 3.1 49.8 + - + +
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Residues in contact with PHE 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I SER* 2.9 42.4 + - - +
106I LEU 4.2 2.9 - - - +
108I GLU* 1.4 74.4 - - + +
110I PHE* 1.3 67.0 + - - +
112I ASP* 3.1 23.1 + - + +
113I LEU* 3.2 18.3 + - + +
200I LEU* 6.1 1.3 - - + -
202I SER* 3.8 28.5 - - - +
203I LEU* 3.2 43.1 - - + -
204I ALA* 4.2 11.9 - - + -
210I ALA 4.3 12.3 - - - -
81P LEU* 4.8 2.2 - - + -
85P TYR* 3.5 41.3 - + - -
299P PRO* 4.8 5.6 - - + -
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Residues in contact with PHE 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I LEU* 3.4 17.7 + - + +
107I ALA* 3.8 5.4 - - - +
108I GLU 3.3 0.4 - - - -
109I PHE* 1.3 79.7 - - - +
111I GLU* 1.4 54.3 + - - +
113I LEU* 3.3 28.1 + - + +
114I ALA* 2.8 24.9 + - - +
198I LEU* 3.8 19.7 - - + -
200I LEU* 3.6 36.8 - - + -
93S HIS* 3.2 28.3 - - + +
94S ALA* 3.5 22.0 - - + +
97S TRP* 3.5 45.1 - + + -
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Residues in contact with GLU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I ALA* 3.1 22.4 + - - +
108I GLU* 3.3 27.5 - - - +
109I PHE 3.2 0.2 - - - -
110I PHE* 1.4 73.7 - - - +
112I ASP* 1.4 60.8 + - - +
114I ALA* 3.3 16.8 + - + +
115I ASP* 2.8 18.9 - - - +
293P SER* 3.2 38.8 + - - +
294P GLY* 3.4 15.3 + - - -
295P THR 5.1 0.2 - - - +
93S HIS* 3.6 38.7 + - + +
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Residues in contact with ASP 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I GLU* 3.0 19.0 + - - +
109I PHE* 3.1 16.8 + - + +
111I GLU* 1.4 73.5 - - - +
113I LEU* 1.4 61.9 + - - +
115I ASP* 3.2 19.6 + - - +
85P TYR* 4.4 13.5 - - - -
295P THR* 3.1 35.0 + - - +
296P VAL 3.3 13.2 - - - +
297P PRO* 3.5 18.4 - - + +
298P THR 4.2 0.7 + - - -
299P PRO* 4.4 13.2 - - + +
300P LEU* 3.7 25.6 - - + +
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Residues in contact with LEU 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I PHE* 3.2 15.2 + - + +
110I PHE* 3.3 37.4 + - + +
112I ASP* 1.4 77.1 - - - +
114I ALA* 1.4 63.0 + - - +
115I ASP 3.3 1.4 + - - -
116I LYS* 3.4 19.1 + - - +
198I LEU* 5.4 6.1 - - + -
199I ASP 3.3 26.2 - - - +
200I LEU* 4.9 1.1 - - - -
202I SER* 4.7 14.4 - - - +
263P LYS* 4.4 14.1 - - + +
264P GLY* 4.5 10.5 - - - +
300P LEU* 4.2 25.6 - - + -
97S TRP* 4.3 6.3 + - + -
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Residues in contact with ALA 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I PHE 2.8 16.4 + - - +
111I GLU* 3.3 13.6 + - + +
113I LEU* 1.4 72.7 - - - +
115I ASP* 1.4 63.4 + - - +
116I LYS 3.1 2.0 + - - -
117I PRO* 4.4 1.6 - - - +
291P MET* 5.1 3.1 - - - +
293P SER* 5.5 7.2 - - - -
93S HIS* 4.6 5.6 - - + +
97S TRP* 3.0 54.4 + - + -
101S ALA* 5.3 0.9 - - - +
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Residues in contact with ASP 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I GLU 2.8 27.0 - - - +
112I ASP* 3.2 10.4 - - - +
113I LEU 3.2 0.8 - - - -
114I ALA* 1.4 76.9 - - - +
116I LYS* 1.4 66.3 + - + +
117I PRO* 3.7 1.0 - - - +
123P PHE* 6.4 0.2 - - + -
291P MET* 3.5 44.3 - - + +
292P ARG* 3.5 36.2 + - - +
293P SER* 4.0 9.1 + - - +
297P PRO* 3.2 37.0 - - + +
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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
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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