Contacts of the helix formed by residues 137 - 153 (chain I) in PDB entry 1K9O
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 137 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I ASP* 3.0 30.5 + - - +
135I PHE 3.0 1.3 - - - -
136I VAL* 1.3 82.5 - - + +
138I SER* 1.3 55.1 + - - +
139I VAL 3.4 2.2 - - - -
140I GLU* 3.0 39.2 + - + +
141I ALA* 2.5 37.0 + - - +
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Residues in contact with SER 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I PHE 4.0 2.8 + - - -
136I VAL 3.5 5.9 + - - -
137I LYS* 1.3 71.3 - - - +
139I VAL* 1.3 57.0 + - - +
142I ALA* 2.5 41.6 + - - +
163I PRO* 3.6 22.6 + - - -
166I LEU* 3.1 41.2 + - - +
167I ASP* 3.8 5.9 + - - -
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Residues in contact with VAL 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I LYS 3.4 0.6 - - - -
138I SER* 1.3 76.7 - - - +
140I GLU* 1.3 59.0 + - - +
142I ALA* 4.4 0.9 - - - -
143I GLY* 3.4 17.3 + - - -
163I PRO* 4.0 26.2 - - + -
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Residues in contact with GLU 140 (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 LYS* 5.4 2.1 + - - -
133I VAL* 4.7 2.1 - - - +
134I ASP* 3.2 35.0 + - - +
137I LYS* 3.0 38.0 + - + +
139I VAL* 1.3 77.9 - - - +
141I ALA* 1.3 60.1 + - - +
143I GLY* 5.3 0.2 - - - -
144I ALA* 3.2 26.7 + - - +
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Residues in contact with ALA 141 (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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133I VAL* 3.7 20.5 - - + +
134I ASP 2.9 31.9 - - - +
135I PHE* 4.0 9.4 - - + -
137I LYS 2.5 14.6 + - - +
138I SER 4.0 1.3 - - - +
140I GLU* 1.3 73.8 + - - +
142I ALA* 1.3 60.3 + - - +
144I ALA* 3.5 2.3 + - - +
145I ILE* 3.1 31.4 + - - +
166I LEU* 4.1 11.2 - - + -
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Residues in contact with ALA 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I SER 2.5 25.3 + - - +
139I VAL* 4.4 1.3 - - - -
141I ALA* 1.3 71.1 - - - +
143I GLY* 1.3 62.3 + - - +
145I ILE 3.5 0.7 + - - -
146I ASN* 3.0 34.3 + - - +
161I VAL* 3.7 18.9 - - + +
163I PRO* 3.9 26.0 - - + -
166I LEU* 3.6 17.8 - - + +
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Residues in contact with GLY 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I VAL 3.4 17.3 + - - -
140I GLU 4.3 0.2 - - - -
141I ALA 3.3 0.6 - - - -
142I ALA* 1.3 78.2 - - - +
144I ALA* 1.3 57.6 + - - +
146I ASN* 3.4 9.4 + - - +
147I LYS* 3.0 32.7 + - - +
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Residues in contact with ALA 144 (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 TYR* 4.4 4.0 + - - -
131I GLN* 5.0 6.6 - - - +
133I VAL* 4.2 16.2 - - + -
140I GLU 3.2 20.9 + - - +
141I ALA 3.7 6.3 - - - +
142I ALA 3.3 0.2 - - - -
143I GLY* 1.3 74.8 - - - +
145I ILE* 1.3 60.7 + - + +
147I LYS* 3.8 7.4 - - - +
148I TRP* 3.5 19.6 + - - +
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Residues in contact with ILE 145 (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 TYR* 3.9 41.6 + - + -
133I VAL* 4.8 1.8 - - + -
135I PHE* 4.4 20.9 - - + -
141I ALA 3.1 19.9 + - - +
142I ALA* 3.7 4.7 - - - +
143I GLY 3.2 0.2 - - - -
144I ALA* 1.3 75.4 - - + +
146I ASN* 1.3 66.4 + - - +
147I LYS 3.1 1.6 - - - -
148I TRP* 3.2 3.8 + - - +
149I VAL* 3.1 30.2 + - + +
160I LEU* 4.8 0.9 - - + -
161I VAL* 3.7 19.5 - - + -
166I LEU* 5.0 4.3 - - + -
173I VAL* 5.0 6.1 - - + -
175I VAL* 3.4 37.9 - - + -
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Residues in contact with ASN 146 (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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142I ALA* 3.0 19.7 + - - +
143I GLY* 3.8 8.2 - - - +
145I ILE* 1.3 75.3 - - - +
147I LYS* 1.3 52.8 + - - +
149I VAL* 3.7 6.9 - - - +
150I GLU* 2.7 40.0 + - + +
157I ILE 4.4 1.9 - - - +
158I LYS* 5.1 0.8 - - - -
159I ASN* 3.8 26.0 + - - +
160I LEU* 3.2 11.7 + - - +
161I VAL* 3.1 45.5 + - - +
163I PRO* 6.2 0.2 - - - +
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Residues in contact with LYS 147 (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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143I GLY 3.0 18.7 + - - +
144I ALA* 3.8 8.7 - - - +
145I ILE 3.1 0.2 - - - -
146I ASN* 1.3 77.3 - - - +
148I TRP* 1.3 60.2 + - - +
150I GLU* 2.9 31.3 + - - +
151I ASP* 2.8 67.3 + - - +
155I ASN* 4.8 5.5 + - - +
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Residues in contact with TRP 148 (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 ALA* 4.1 11.4 - - + -
104I SER* 3.7 27.8 - - - -
105I LYS* 3.3 52.2 - - + +
107I TYR* 3.3 30.7 - - - +
128I SER* 6.0 2.9 - - - -
131I GLN* 5.6 4.7 - - - +
144I ALA 3.5 8.5 + - - +
145I ILE 3.2 4.0 + - - +
147I LYS* 1.3 77.4 - - - +
149I VAL* 1.3 70.9 + - + +
151I ASP* 3.9 6.4 - - + +
152I GLN* 3.0 70.6 + - + +
175I VAL* 4.6 6.1 - - + -
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I ALA* 5.8 0.7 - - - -
145I ILE* 3.1 19.2 + - + +
146I ASN* 3.8 6.7 - - - +
148I TRP* 1.3 94.2 - - + +
150I GLU* 1.3 51.2 + - - +
152I GLN* 3.5 3.8 + - - +
153I THR* 2.7 37.6 + - - +
157I ILE* 3.6 23.6 - - + +
160I LEU* 3.9 20.9 - - + -
175I VAL* 4.3 18.8 - - + -
177I ALA* 3.6 29.4 - - + -
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Residues in contact with GLU 150 (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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146I ASN* 2.7 25.3 + - - +
147I LYS* 2.9 30.0 + - - +
149I VAL* 1.3 74.6 - - - +
151I ASP* 1.3 61.7 + - - +
153I THR* 3.9 2.0 - - - -
154I ASN 3.4 0.5 + - - -
155I ASN* 2.5 67.8 + - - +
157I ILE 3.6 7.8 + - - +
158I LYS* 3.1 40.0 + - + +
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Residues in contact with ASP 151 (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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147I LYS* 2.8 57.1 + - - +
148I TRP* 4.0 7.7 - - + +
150I GLU* 1.3 79.6 - - - +
152I GLN* 1.3 65.5 + - + +
153I THR 3.3 1.0 + - - -
154I ASN* 3.9 12.4 + - - +
155I ASN* 4.5 4.8 - - - +
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Residues in contact with GLN 152 (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 LYS* 3.8 19.1 - - - +
102I MET 5.2 3.0 + - - -
103I ALA* 4.1 22.8 - - + +
148I TRP* 3.0 65.2 + - + +
149I VAL* 4.0 4.5 - - - +
151I ASP* 1.3 80.6 - - - +
153I THR* 1.3 59.6 + - - +
154I ASN* 3.6 2.5 + - - -
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Residues in contact with THR 153 (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 LYS* 3.6 26.0 + - + +
103I ALA* 5.2 1.8 - - + -
149I VAL 2.7 22.2 + - - +
150I GLU* 3.9 1.7 - - - -
151I ASP 3.3 0.2 - - - -
152I GLN* 1.3 83.0 - - + +
154I ASN* 1.3 71.4 + - - +
156I ARG* 3.0 24.9 + - - +
157I ILE* 3.0 51.2 + - + +
177I ALA* 4.1 13.5 - - + +
179I TYR* 4.6 2.0 - - + -
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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