Contacts of the helix formed by residues 141 - 159 (chain T) 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 LEU 141 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128T PHE* 3.4 34.8 - - + +
129T LEU 4.2 3.4 - - - +
131T THR* 3.7 38.8 - - - +
137T THR* 2.8 32.0 + - + +
138T LYS* 2.9 8.2 + - - +
140T GLN* 1.3 77.6 - - - +
142T ILE* 1.3 59.5 + - - +
143T LEU 3.1 0.9 - - - -
144T ALA* 3.8 9.0 - - + +
145T ARG* 2.9 30.0 + - - +
174T TYR* 3.6 29.9 - - + +
177T ASP* 5.3 1.3 - - + +
182T LEU* 4.6 7.8 - - + +
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Residues in contact with ILE 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138T LYS 3.2 4.6 + - - -
139T GLN* 3.2 37.0 - - + +
141T LEU* 1.3 76.3 - - - +
143T LEU* 1.3 70.5 + - + +
145T ARG* 3.9 5.3 + - - +
146T ASP* 3.2 28.4 + - - +
178T TYR* 3.6 32.1 - - + +
182T LEU* 4.0 14.9 - - + +
183T PRO* 3.8 28.3 - - + -
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Residues in contact with LEU 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T LEU* 3.6 37.0 - - + +
95T TYR* 5.1 6.3 + - - +
139T GLN 3.4 19.1 - - - +
140T GLN* 3.9 14.9 + - - +
141T LEU 3.1 0.4 - - - -
142T ILE* 1.3 90.0 - - + +
144T ALA* 1.3 57.7 + - - +
146T ASP* 4.3 13.5 - - - +
147T ILE* 3.4 22.9 + - - +
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Residues in contact with ALA 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T LEU* 5.3 0.7 - - + -
123T LEU* 4.2 26.5 - - + +
128T PHE* 4.6 8.1 - - + -
140T GLN 3.3 18.0 + - - +
141T LEU* 3.6 16.5 + - + -
143T LEU* 1.3 75.1 - - - +
145T ARG* 1.3 63.3 + - - +
146T ASP 3.5 0.4 - - - -
147T ILE* 3.6 16.7 + - - +
148T LEU* 3.5 20.5 - - - +
174T TYR* 6.4 0.9 - - - -
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Residues in contact with ARG 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141T LEU* 2.9 20.2 + - - +
142T ILE 4.0 3.9 + - - +
143T LEU 3.5 0.4 - - - -
144T ALA* 1.3 75.9 - - - +
146T ASP* 1.3 74.5 + - - +
148T LEU* 2.9 20.4 + - - +
149T GLU* 3.0 51.3 + - - +
171T LEU* 4.3 9.1 - - + +
174T TYR* 3.8 42.2 - - + -
175T TYR* 3.5 19.5 - - - -
178T TYR* 2.6 58.0 + - - -
182T LEU* 5.7 0.9 - - - -
185T SER* 3.4 13.7 + - - -
188T MET* 4.8 1.6 - - - +
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Residues in contact with ASP 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95T TYR* 4.5 23.4 + - + -
142T ILE* 3.2 21.6 - - - +
143T LEU* 4.3 15.3 - - - +
144T ALA 3.5 0.2 - - - -
145T ARG* 1.3 84.8 + - - +
147T ILE* 1.3 55.6 + - - +
148T LEU 2.8 0.2 + - - -
149T GLU* 2.7 43.6 + - - +
150T ILE* 3.0 25.8 + - + +
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Residues in contact with ILE 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T VAL* 6.5 0.2 - - + -
88T LEU* 4.8 9.2 - - + +
91T ALA* 3.6 22.4 - - + -
95T TYR* 3.8 24.7 - - + -
116T LEU* 4.2 37.6 - - + +
119T LEU* 5.2 4.5 - - + -
120T LYS* 5.3 1.1 - - - +
123T LEU* 3.7 36.6 - - + -
143T LEU 3.4 22.2 - - - +
144T ALA* 3.6 10.3 + - - +
145T ARG 3.2 0.6 - - - -
146T ASP* 1.3 73.6 - - - +
148T LEU* 1.3 65.3 + - + +
150T ILE* 5.8 0.7 - - - -
151T GLY* 4.0 14.0 + - - +
167T TYR* 5.2 1.2 - - - -
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Residues in contact with LEU 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116T LEU 5.9 0.9 - - - +
120T LYS* 5.4 20.0 - - + +
123T LEU* 5.2 5.4 - - + -
144T ALA 3.5 18.2 - - - +
145T ARG* 2.9 6.6 + - - +
147T ILE* 1.3 93.5 - - + +
149T GLU* 1.3 59.5 + - - +
150T ILE 3.6 0.2 - - - -
152T ALA* 2.9 32.5 + - - +
167T TYR* 3.8 22.4 - - + -
170T GLN* 4.2 26.9 - - + +
171T LEU* 3.9 15.2 - - + +
174T TYR* 4.2 21.8 - - + -
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Residues in contact with GLU 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145T ARG* 3.0 44.9 + - - +
146T ASP* 2.7 38.1 + - - +
148T LEU* 1.3 70.3 - - - +
150T ILE* 1.3 62.0 + - + +
151T GLY 3.0 0.4 - - - -
152T ALA* 2.8 20.8 + - - +
153T GLN* 3.0 16.3 + - - +
171T LEU* 4.3 8.7 - - + +
175T TYR* 4.2 5.2 - - - +
187T TYR* 3.4 43.1 - - + +
191T LEU* 3.9 21.7 - - + +
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Residues in contact with ILE 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95T TYR* 4.2 41.1 - - + +
98T LEU* 3.5 30.3 - - + +
99T LYS* 4.3 22.9 - - + +
102T TRP* 3.7 34.4 - - + -
116T LEU* 5.2 0.7 - - + -
146T ASP* 3.0 18.1 + - + +
147T ILE* 5.8 0.4 - - - -
149T GLU* 1.3 82.6 - - + +
151T GLY* 1.3 57.7 + - - +
153T GLN* 4.1 3.4 - - - -
154T TRP 3.9 4.0 + - - -
187T TYR* 4.9 11.9 - - + +
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Residues in contact with GLY 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T LEU* 4.8 6.5 - - - -
113T GLY* 6.1 1.8 - - - -
116T LEU* 4.9 11.5 - - - +
147T ILE 4.0 13.2 + - - -
148T LEU 3.7 5.4 + - - -
149T GLU 3.0 1.4 - - - -
150T ILE* 1.3 78.0 - - - +
152T ALA* 1.3 53.1 + - - +
153T GLN 3.3 0.4 - - - -
154T TRP* 3.5 3.9 + - - +
155T SER* 2.5 34.5 + - - -
158T ARG* 3.9 6.2 + - - -
167T TYR* 4.2 9.9 - - - -
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Residues in contact with ALA 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148T LEU 2.9 20.1 + - - +
149T GLU 2.8 4.8 + - - +
151T GLY* 1.3 75.4 - - - +
153T GLN* 1.3 60.7 + - - +
155T SER* 2.8 27.0 + - - -
156T ILE* 3.0 19.1 + - + +
164T PHE* 5.0 0.8 - - + +
167T TYR* 3.8 22.8 - - + -
168T MET* 6.4 1.1 - - + -
171T LEU* 4.2 13.7 - - + -
191T LEU* 5.4 5.2 - - + -
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Residues in contact with GLN 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T TRP* 3.6 28.2 - - + -
149T GLU 3.0 13.6 + - - +
150T ILE 4.3 0.2 - - - +
152T ALA* 1.3 77.6 - - - +
154T TRP* 1.3 60.0 + - - +
156T ILE* 3.3 22.6 + - - +
157T LEU* 3.6 16.1 + - - +
187T TYR* 4.0 26.0 + - + +
190T GLN 5.7 0.4 + - - -
191T LEU* 3.2 32.6 - - + +
194T LEU* 3.8 17.9 - - - +
255T SER* 3.7 20.2 + - - -
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Residues in contact with TRP 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T LEU* 4.3 24.2 - - + -
102T TRP* 4.0 4.3 - - + -
106T SER 5.6 1.6 - - - -
109T LEU* 3.4 48.5 - - + -
110T SER* 3.4 37.6 + - - +
113T GLY* 4.2 13.9 - - - -
114T GLU* 5.8 0.2 - - - +
150T ILE 3.9 2.6 + - - -
151T GLY* 3.5 6.5 + - - +
152T ALA 3.2 0.4 - - - -
153T GLN* 1.3 73.8 - - - +
155T SER* 1.3 60.6 + - - +
156T ILE 3.1 1.8 - - - -
157T LEU* 3.9 25.8 - - + +
158T ARG* 2.9 77.9 + - + +
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Residues in contact with SER 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151T GLY 2.5 22.9 + - - -
152T ALA* 2.8 14.9 + - - -
154T TRP* 1.3 77.7 - - - +
156T ILE* 1.3 59.7 + - - +
158T ARG* 3.2 19.0 + - - +
159T LYS 3.3 16.3 + - - +
163T SER* 4.4 3.8 - - - -
164T PHE* 3.5 25.1 + - - +
167T TYR* 3.2 34.0 - - - -
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Residues in contact with ILE 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T ALA* 3.0 17.3 + - + +
153T GLN* 3.5 18.2 - - - +
154T TRP 3.1 0.4 - - - -
155T SER* 1.3 74.2 - - - +
157T LEU* 1.3 69.7 + - + +
159T LYS* 2.8 31.0 + - - +
164T PHE* 3.8 25.8 - - + -
168T MET* 5.0 9.0 - - + -
191T LEU* 5.7 1.8 - - + -
194T LEU* 3.5 36.6 - - + -
255T SER* 5.9 2.0 - - - +
258T PHE* 5.8 3.8 - - + -
259T PHE* 4.5 28.9 - - + -
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Residues in contact with LEU 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T TRP* 3.9 27.6 - - + +
109T LEU* 5.6 0.9 - - + -
153T GLN* 3.6 20.8 + - - +
154T TRP* 3.5 27.5 + - + -
156T ILE* 1.3 83.5 - - + +
158T ARG* 1.3 60.4 + - - +
159T LYS* 3.3 17.4 - - - +
258T PHE* 4.0 34.8 - - + -
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Residues in contact with ARG 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T SER* 5.8 1.6 - - - -
113T GLY* 3.2 32.1 + - - -
114T GLU* 4.1 11.1 - - - +
117T GLY* 6.0 0.4 - - - -
151T GLY* 3.9 4.0 + - - -
154T TRP* 2.9 54.4 + - + +
155T SER* 3.2 32.0 + - - +
156T ILE 3.1 0.2 - - - -
157T LEU* 1.3 74.6 - - - +
159T LYS* 1.3 74.4 + - - +
163T SER* 5.5 6.0 - - - +
167T TYR* 4.2 12.1 + - - -
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Residues in contact with LYS 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155T SER 3.3 2.8 + - - -
156T ILE 2.8 19.0 + - - +
157T LEU* 3.5 15.5 - - - +
158T ARG* 1.3 90.4 - - - +
160T ASP* 1.3 73.9 + - - +
163T SER* 3.4 12.6 + - - -
164T PHE* 3.9 8.5 - - + -
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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