Contacts of the helix formed by residues 135 - 154 (chain L) 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 ASN 135 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ILE* 4.7 6.1 - - - +
78L SER* 2.9 32.0 + - - -
80L GLU* 3.5 33.4 + - - +
130L LEU* 3.0 38.1 + - - +
132L SER* 3.5 7.4 - - - +
133L SER 2.9 3.2 + - - +
134L SER* 1.3 78.4 - - - +
136L PHE* 1.3 57.7 + - - +
137L GLU 3.3 0.7 - - - -
138L ALA* 3.4 5.1 + - - +
139L THR* 2.6 42.0 + - - -
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Residues in contact with PHE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L LEU* 4.1 17.0 - - + -
75L ILE* 4.8 10.5 - - + -
130L LEU 4.8 2.2 - - - +
131L LEU* 4.3 15.7 - - + +
132L SER 3.4 10.6 + - - +
133L SER* 4.6 4.5 - - - -
135L ASN* 1.3 80.5 - - - +
137L GLU* 1.3 73.9 + - - +
139L THR* 3.6 5.2 - - - -
140L LYS* 2.8 47.8 + - + +
187L LEU 3.9 16.8 - - - -
188L VAL* 3.8 8.1 - - + -
189L VAL* 3.6 45.5 - - + -
192L LEU* 3.5 34.3 - - + -
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Residues in contact with GLU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L SER* 3.9 20.2 - - - +
134L SER* 4.3 9.6 - - - +
135L ASN 3.3 1.4 - - - +
136L PHE* 1.3 96.9 - - + +
138L ALA* 1.3 56.6 + - - +
140L LYS* 4.0 12.9 + - - +
141L LYS* 3.1 39.1 + - - +
188L VAL* 6.2 0.5 - - - +
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Residues in contact with ALA 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L SER 3.5 20.9 + - - +
135L ASN* 3.4 7.7 + - - +
136L PHE 3.2 0.4 - - - -
137L GLU* 1.3 78.4 - - - +
139L THR* 1.3 63.6 + - - +
141L LYS* 3.6 7.6 + - - +
142L SER* 3.1 25.6 + - - -
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Residues in contact with THR 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L LEU* 4.2 6.5 - - + +
74L ASN* 3.6 31.9 + - + +
75L ILE* 3.5 34.7 - - + +
78L SER* 4.3 6.2 + - - -
135L ASN* 2.6 30.7 + - - -
136L PHE* 3.6 4.9 - - - -
138L ALA* 1.3 79.5 - - - +
140L LYS* 1.3 62.7 + - - +
142L SER* 3.1 7.9 + - - -
143L VAL* 3.1 28.8 + - + +
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Residues in contact with LYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L LEU* 4.2 21.5 - - + +
136L PHE* 2.8 37.9 + - + +
137L GLU* 4.0 15.8 + - - +
139L THR* 1.3 70.6 - - - +
141L LYS* 1.3 65.6 + - - +
142L SER 3.1 1.6 - - - -
143L VAL* 3.4 2.5 + - + +
144L LEU* 3.0 35.5 + - + +
184L LEU* 3.6 20.9 - - + +
185L GLU* 3.0 32.6 + - - +
186L ASN 4.5 0.8 - - - -
187L LEU 3.0 25.1 + - - +
188L VAL* 5.1 4.2 - - - +
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Residues in contact with LYS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L GLU* 3.1 28.1 + - - +
138L ALA* 4.0 6.8 - - - +
139L THR 3.4 0.2 - - - -
140L LYS* 1.3 77.0 - - - +
142L SER* 1.3 59.7 + - - +
144L LEU* 3.8 10.3 + - + +
145L LYS* 3.5 20.4 + - - +
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Residues in contact with SER 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L ASN* 6.0 1.1 - - - -
138L ALA 3.1 13.2 + - - -
139L THR* 3.1 11.6 + - - -
140L LYS 3.1 0.6 - - - -
141L LYS* 1.3 78.4 - - - +
143L VAL* 1.3 61.9 + - - +
144L LEU 3.3 0.7 - - - -
145L LYS* 3.9 6.6 - - - +
146L GLN* 3.0 27.8 + - - +
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Residues in contact with VAL 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L GLY 5.9 0.2 - - - +
70L ASN* 4.5 11.2 - - - +
71L LEU* 3.6 28.5 - - + -
74L ASN* 3.4 44.0 - - + +
139L THR 3.1 14.4 + - - +
140L LYS* 3.7 7.6 - - + +
142L SER* 1.3 75.6 - - - +
144L LEU* 1.3 66.0 + - + +
145L LYS 3.1 1.8 - - - -
146L GLN* 3.6 8.3 - - + +
147L VAL* 2.8 33.1 + - - +
184L LEU* 3.8 20.6 - - + +
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Residues in contact with LEU 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L LYS* 3.0 28.9 + - + +
141L LYS* 3.9 10.5 - - + +
143L VAL* 1.3 81.1 - - + +
145L LYS* 1.3 57.5 + - - +
147L VAL* 4.3 2.5 - - - +
148L GLN* 3.3 23.2 + - - +
181L LEU* 4.3 19.4 - - + +
184L LEU* 3.5 38.4 - - + +
185L GLU* 3.6 40.8 - - + +
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Residues in contact with LYS 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141L LYS 3.5 15.0 + - - +
142L SER* 3.9 6.1 - - - +
144L LEU* 1.3 78.0 - - - +
146L GLN* 1.3 59.6 + - - +
147L VAL 3.2 1.6 - - - -
148L GLN* 2.9 14.6 + - + +
149L ASP* 2.8 50.0 + - - +
291M ASP* 5.6 4.4 + - - -
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Residues in contact with GLN 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L ASN* 4.3 13.6 + - - +
73L LYS* 5.7 2.8 - - - +
74L ASN* 3.1 36.0 + - - +
142L SER* 3.0 19.6 + - - +
143L VAL* 3.6 9.4 - - - +
145L LYS* 1.3 81.2 - - - +
147L VAL* 1.3 61.2 + - - +
149L ASP* 3.4 9.1 + - - +
150L PHE* 3.3 19.9 + - - +
178L ARG* 5.8 2.8 - - - +
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Residues in contact with VAL 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L ASN* 4.0 10.1 - - - +
143L VAL 2.8 20.3 + - - +
144L LEU* 4.5 2.5 - - - +
146L GLN* 1.3 75.6 - - + +
148L GLN* 1.3 64.5 + - - +
149L ASP 3.2 0.2 - - - -
150L PHE* 3.3 9.9 + - + +
151L GLU* 3.2 27.4 + - + +
178L ARG* 3.7 38.8 - - + +
179L GLY 4.0 15.7 - - - +
181L LEU* 4.5 22.9 - - + +
184L LEU* 4.0 9.0 - - + -
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Residues in contact with GLN 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L LEU 3.3 19.5 + - - +
145L LYS* 2.9 14.5 + - - +
147L VAL* 1.3 77.9 - - - +
149L ASP* 1.3 62.7 + - - +
151L GLU* 3.9 3.0 + - - +
152L ASP* 3.4 32.7 + - - +
181L LEU* 4.3 25.1 - - + +
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Residues in contact with ASP 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L LYS* 2.8 38.9 + - - +
146L GLN* 3.4 13.5 - - - +
148L GLN* 1.3 78.7 + - - +
150L PHE* 1.3 56.7 + - - +
152L ASP* 3.4 1.1 + - - -
153L ASN* 2.9 53.4 + - - +
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Residues in contact with PHE 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L GLN 3.3 10.6 + - - +
147L VAL* 3.6 15.7 - - + +
148L GLN 3.3 0.2 - - - -
149L ASP* 1.3 81.8 - - - +
151L GLU* 1.3 69.8 + - - +
154L ASP* 3.1 57.8 + - + +
157L ASN* 3.9 11.2 - - + -
158L ARG* 3.8 29.6 - - + -
161L GLU* 4.6 3.4 - - + -
178L ARG* 3.2 57.9 - - + +
34P TYR* 3.9 20.6 - - - -
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Residues in contact with GLU 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L VAL* 3.2 17.6 + - + +
148L GLN* 4.4 5.2 - - - +
149L ASP 3.4 0.2 - - - -
150L PHE* 1.3 87.7 - - - +
152L ASP* 1.3 60.9 + - - +
158L ARG* 3.3 41.9 + - - +
162L HIS* 3.1 27.4 - - - -
181L LEU* 5.4 9.0 - - + -
33P THR* 4.2 4.9 + - - +
34P TYR* 3.1 31.0 + - - -
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Residues in contact with ASP 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L GLN* 3.4 28.9 + - - +
149L ASP* 3.4 4.4 + - - +
150L PHE 3.2 0.4 - - - -
151L GLU* 1.3 83.1 - - - +
153L ASN* 1.3 71.6 + - - +
155L HIS* 3.5 17.8 + - - -
158L ARG* 4.9 0.6 + - - +
255L LEU* 5.6 0.5 - - - +
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Residues in contact with ASN 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L ASP* 2.9 43.5 + - - +
150L PHE 3.6 0.4 + - - -
152L ASP* 1.3 91.8 - - - +
154L ASP* 1.3 61.0 + - - +
155L HIS* 2.9 27.6 + - - -
156L PRO* 4.9 0.9 - - - +
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Residues in contact with ASP 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L ASP 4.2 0.4 + - - -
150L PHE* 3.1 35.6 + - + +
153L ASN* 1.3 72.6 - - - +
155L HIS* 1.3 56.9 + - - +
156L PRO* 3.3 14.2 - - - +
157L ASN* 2.8 41.8 + - - +
158L ARG* 2.9 29.3 + - - +
178L ARG* 5.4 0.3 + - - -
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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
------------------------------------------------------------
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