Contacts of the helix formed by residues 123 - 143 (chain F) in PDB entry 1KYO
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 CYS 123 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D PRO* 4.2 4.9 - - - -
204D ALA* 2.9 16.0 + - + +
98F TYR* 3.8 22.1 - - + -
101F CYS* 2.0 63.3 - - + -
102F ALA 3.6 2.0 - - - -
105F VAL* 3.6 12.1 - - - -
122F ASP* 1.3 75.3 - - - +
124F VAL* 1.3 54.4 + - - +
125F GLU 3.2 2.2 - - - -
126F GLU* 3.0 8.9 + - - +
127F PHE* 2.8 33.6 + - - +
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ALA* 4.0 24.5 - - + -
203D PRO* 4.3 2.2 - - + -
206D VAL* 3.5 25.4 - - + -
214D TYR* 3.5 26.5 - - + +
122F ASP* 3.4 30.7 + - + +
123F CYS* 1.3 74.3 - - - +
125F GLU* 1.3 61.1 + - - +
127F PHE* 3.5 5.3 - - - +
128F PHE* 2.8 54.7 + - + -
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 6.3 2.7 - - - -
122F ASP* 4.9 2.2 + - - +
123F CYS* 3.2 0.4 - - - +
124F VAL* 1.3 78.2 - - - +
126F GLU* 1.3 69.0 + - - +
128F PHE* 3.1 9.0 + - - +
129F HIS* 2.7 53.6 + - + -
81H TYR 5.2 0.2 - - - +
82H SER* 3.8 12.8 - - - -
83H LYS* 2.9 52.7 + - + +
84H ALA 4.8 0.7 + - - -
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Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU 5.1 1.6 - - - +
97F HIS* 4.1 21.1 - - + +
98F TYR* 4.0 25.9 - - + +
101F CYS* 3.6 10.2 - - + +
104F ARG* 4.9 2.9 + - - -
123F CYS* 3.0 19.9 - - + +
125F GLU* 1.3 80.0 - - + +
127F PHE* 1.3 62.5 + - - +
129F HIS* 3.4 10.9 + - + +
130F LEU* 3.3 21.1 + - - +
83H LYS* 2.7 43.8 + - - +
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Residues in contact with PHE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D PRO* 3.5 31.6 - - + -
201D GLU 5.2 5.4 - - - -
203D PRO* 4.0 22.7 - - + -
214D TYR* 4.4 11.0 - + - -
216D PRO* 4.1 23.3 - - + -
98F TYR* 4.1 23.9 - + + -
123F CYS 2.8 19.1 + - - +
124F VAL 3.5 4.3 - - - +
125F GLU 3.2 0.2 - - - -
126F GLU* 1.3 75.5 - - - +
128F PHE* 1.3 74.9 + + - +
130F LEU* 3.3 15.2 + - + +
131F GLN* 2.8 55.8 + - + +
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Residues in contact with PHE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 3.6 41.1 - - + -
65D ALA* 4.1 9.2 - - - -
68D GLY 4.1 0.4 - - - -
69D LEU* 3.7 35.1 - - + +
214D TYR* 3.3 24.7 - - - -
216D PRO* 3.7 31.6 - - + -
221D GLY* 6.2 1.1 - - - -
124F VAL* 2.8 33.1 + - + +
125F GLU* 3.4 7.2 - - - +
127F PHE* 1.3 82.0 - + - +
129F HIS* 1.3 56.2 + - + +
131F GLN* 3.5 4.3 - - - +
132F HIS* 2.7 37.4 + - - +
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Residues in contact with HIS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 4.2 12.8 - - + +
125F GLU* 2.7 55.8 + - + -
126F GLU* 3.6 10.8 - - + +
127F PHE 3.3 0.2 - - - -
128F PHE* 1.3 76.0 - - + +
130F LEU* 1.3 63.2 + - - +
132F HIS* 3.3 6.9 + - - +
133F TYR* 3.1 23.7 + - - +
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F LYS* 4.9 12.1 - - + +
91F GLY* 4.7 2.5 - - - +
94F LEU* 4.3 28.0 - - + +
95F VAL* 4.3 33.0 - - + +
98F TYR* 4.9 16.2 - - + -
126F GLU 3.3 9.4 + - - +
127F PHE* 3.5 19.1 - - + +
129F HIS* 1.3 78.1 - - - +
131F GLN* 1.3 66.4 + - - +
132F HIS 3.2 0.7 + - - -
133F TYR* 3.3 6.8 + - + +
134F LEU* 3.2 46.3 + - + +
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Residues in contact with GLN 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LEU* 4.4 12.8 - - + -
197D GLY* 5.3 3.0 + - - -
199D PRO* 5.4 2.7 - - - +
216D PRO* 4.7 5.5 - - + +
217D TYR* 3.5 29.6 + - + +
82F ARG* 3.7 27.9 - - - +
127F PHE* 2.8 48.5 + - + +
128F PHE* 3.7 8.1 - - + +
130F LEU* 1.3 80.7 - - - +
132F HIS* 1.3 55.6 + - - +
134F LEU* 3.7 17.1 + - - +
135F ASP* 3.1 34.1 + - - +
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Residues in contact with HIS 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.8 16.0 - - + +
70D HIS* 5.5 14.7 + - + +
128F PHE 2.7 21.8 + - - +
129F HIS* 3.6 7.4 - - - +
130F LEU 3.1 0.2 - - - -
131F GLN* 1.3 71.7 - - - +
133F TYR* 1.3 68.8 + - - +
135F ASP* 3.0 12.2 + - + +
136F THR* 2.9 43.3 + - - +
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Residues in contact with TYR 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F PHE* 3.2 47.5 + + + -
88F THR* 2.9 21.5 + - - +
90F GLU* 3.6 33.9 + - + +
91F GLY* 3.7 9.9 - - - -
94F LEU* 3.5 31.2 - - + -
129F HIS 3.1 7.0 + - - +
130F LEU* 3.7 3.1 - - + +
132F HIS* 1.3 80.7 - - - +
134F LEU* 1.3 74.8 + - + +
136F THR* 3.4 9.0 + - - -
137F ALA* 3.1 26.4 + - + +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ARG* 4.0 41.7 - - + +
85F PHE* 4.0 18.4 - - + -
86F LYS* 4.1 18.6 - - + +
130F LEU* 3.2 36.8 + - + +
131F GLN* 3.7 22.7 - - - +
132F HIS 3.2 0.4 - - - -
133F TYR* 1.3 90.8 - - + +
135F ASP* 1.3 57.8 + - - +
137F ALA* 3.1 4.2 + - - +
138F THR* 2.7 40.8 + - + +
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Residues in contact with ASP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 3.3 21.7 - - - +
70D HIS 4.1 1.4 - - - +
72D PRO* 3.8 28.0 - - + +
74D TYR* 4.4 3.6 + - - -
217D TYR* 2.8 32.2 + - - -
82F ARG* 4.3 8.0 + - - -
131F GLN* 3.1 20.0 + - - +
132F HIS* 3.0 14.2 + - + +
134F LEU* 1.3 76.4 - - - +
136F THR* 1.3 58.0 + - - +
138F THR* 3.6 6.1 + - - -
139F ALA* 2.9 38.2 + - - +
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PRO* 5.8 0.7 - - - -
132F HIS* 2.9 36.9 + - - +
133F TYR* 3.5 10.4 - - - -
135F ASP* 1.3 75.7 - - - +
137F ALA* 1.3 59.8 + - - +
139F ALA* 4.5 2.6 - - - +
140F PRO* 3.4 17.5 - - - +
141F ARG* 5.3 0.5 + - - -
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F PHE* 3.6 39.5 - - + -
133F TYR* 3.1 21.9 + - + +
134F LEU* 3.5 5.4 - - - +
135F ASP 3.1 0.2 - - - -
136F THR* 1.3 80.3 - - - +
138F THR* 1.3 61.1 + - - +
139F ALA 3.7 0.3 + - - -
140F PRO* 3.7 4.7 - - - +
141F ARG* 2.9 35.3 + - - +
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Residues in contact with THR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 4.5 5.8 + - - -
78F LEU* 3.9 21.3 - - + +
81F LEU* 3.8 38.6 - - + +
82F ARG* 4.2 16.2 + - + +
85F PHE* 4.5 6.5 - - + -
134F LEU* 2.7 27.7 + - - +
135F ASP* 3.6 9.5 + - - -
137F ALA* 1.3 72.4 - - - +
139F ALA* 1.3 66.4 + - - +
141F ARG* 3.2 5.7 + - - +
142F LEU* 2.9 28.5 + - - +
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PRO* 3.9 20.0 - - + -
73D ALA 3.8 21.1 - - - +
74D TYR* 3.5 32.0 - - + -
75D ALA* 4.4 3.1 + - - +
135F ASP 2.9 20.4 + - - +
136F THR* 4.5 2.0 - - - +
138F THR* 1.3 78.8 + - - +
140F PRO* 1.3 69.4 - - + +
142F LEU* 4.0 3.8 + - - +
143F PHE* 4.7 2.3 + - - +
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Residues in contact with PRO 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA 5.2 3.4 - - - +
75D ALA* 5.1 12.9 - - + +
136F THR 3.4 17.5 - - - +
137F ALA 3.7 10.3 - - - +
139F ALA* 1.3 95.8 - - + +
141F ARG* 1.3 71.9 + - + +
143F PHE* 5.1 1.8 + - - +
144F ASP* 3.9 12.5 - - - +
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Residues in contact with ARG 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU* 4.4 20.0 - - + -
85F PHE* 3.6 35.6 - - - -
136F THR 5.3 0.4 + - - -
137F ALA* 2.9 29.6 + - - +
138F THR 3.2 6.1 + - - +
140F PRO* 1.3 89.5 - - + +
142F LEU* 1.3 67.6 + - - +
143F PHE 3.5 0.7 - - - -
144F ASP* 3.0 26.2 + - - +
145F LYS* 4.0 8.3 + - - +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TYR* 3.5 22.7 - - + -
192D PHE* 3.4 33.2 - - + -
245D SER* 4.0 5.8 - - - +
77F GLN* 4.0 11.2 - - + +
78F LEU* 3.7 42.8 - - + +
81F LEU* 3.7 13.1 - - + +
138F THR 2.9 20.2 + - - +
139F ALA 4.0 0.2 + - - -
140F PRO 3.9 0.6 - - - -
141F ARG* 1.3 70.8 - - - +
143F PHE* 1.3 65.2 + - + +
145F LYS* 2.8 28.6 + - - +
146F LEU* 3.6 16.1 + - + -
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Residues in contact with PHE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TYR* 3.9 18.4 - + + -
75D ALA* 3.1 40.2 - - + +
76D TRP* 3.7 46.4 - + - -
77D SER 5.1 0.7 - - - -
192D PHE* 3.8 29.4 - + - -
249D LYS* 3.6 36.2 - - + -
139F ALA 4.7 2.8 + - - +
140F PRO 5.1 1.3 + - - +
141F ARG 3.3 1.2 + - - -
142F LEU* 1.3 82.2 - - + +
144F ASP* 1.3 61.3 + - - +
145F LYS 3.0 1.3 - - - -
146F LEU* 3.1 40.2 + - + +
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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) + - + + + + + -
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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