Contacts of the helix formed by residues 143 - 154 (chain B) in PDB entry 1L8A
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 ILE 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B SER* 3.4 25.8 - - - +
110B PHE* 3.5 35.9 - - + +
113B SER* 3.9 4.9 - - - +
117B TYR* 3.6 38.6 - - + +
139B PHE* 4.4 2.0 - - + -
140B GLN* 3.0 39.3 - - + +
141B GLY 3.2 0.2 + - - -
142B HIS* 1.3 76.9 - - - +
144B SER* 1.3 64.7 + - - +
145B PRO* 3.1 5.4 - - - -
146B GLY* 3.0 15.8 + - - -
147B VAL* 3.5 23.6 + - + -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLN 4.2 0.4 + - - -
141B GLY 3.3 14.7 + - - -
142B HIS 4.5 0.3 - - - -
143B ILE* 1.3 80.3 - - - +
145B PRO* 1.4 67.9 - - - +
147B VAL* 2.9 6.0 + - - +
148B TYR* 2.7 39.3 + - - -
165B PHE* 4.6 0.3 - - - -
176B SER 2.7 27.4 + - - -
177B TYR* 4.4 3.8 - - - -
178B PRO* 4.8 0.2 - - - -
187B TRP* 3.7 31.2 - - - -
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Residues in contact with PRO 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA* 3.7 17.1 - - + +
92B THR* 5.3 6.0 + - + -
93B VAL* 3.9 23.8 - - + -
106B HIS 3.6 22.0 - - - +
110B PHE* 5.7 2.7 - - + -
142B HIS 3.6 10.1 - - - +
143B ILE* 3.1 6.3 - - - -
144B SER* 1.4 97.8 - - - +
146B GLY* 1.3 55.0 + - - +
148B TYR* 3.4 12.2 + - + +
149B ALA* 2.8 29.1 + - - +
165B PHE* 3.9 16.6 - - + -
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Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 3.7 7.4 - - - +
89B ALA* 3.9 6.4 - - - +
110B PHE* 3.4 39.2 - - - -
143B ILE 3.0 9.1 + - - -
145B PRO* 1.3 76.0 - - - +
147B VAL* 1.3 65.4 + - - +
149B ALA* 3.5 3.0 + - - +
150B ARG* 3.1 20.1 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 5.8 0.9 - - + -
117B TYR* 5.6 1.1 - - + -
121B PHE* 5.2 10.1 - - + -
139B PHE* 3.8 30.3 - - + -
143B ILE* 3.5 19.9 + - + +
144B SER* 2.9 8.7 + - - +
146B GLY* 1.3 73.3 - - - +
148B TYR* 1.3 67.5 + - - +
150B ARG* 3.4 5.1 + - - +
151B ALA* 3.0 22.1 + - + +
186B PHE* 4.0 6.7 - - + -
187B TRP* 3.5 28.0 - - + -
463B PRO* 3.6 29.2 - - + -
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 5.6 1.3 - - + -
144B SER* 2.7 28.7 + - - +
145B PRO* 3.6 6.1 - - + +
147B VAL* 1.3 78.3 - - - +
149B ALA* 1.3 56.2 + - - +
151B ALA* 3.3 2.0 + - - +
152B PHE* 3.0 30.5 + - - +
157B LEU* 3.6 21.1 - - + +
162B LEU* 4.0 17.8 - - + +
165B PHE* 3.9 24.0 - + - -
174B LEU* 3.8 17.7 - - + -
175B SER 2.7 30.5 + - - -
177B TYR 4.2 1.0 + - - -
183B MET* 3.4 18.7 - - + -
186B PHE* 3.7 15.0 - + - -
187B TRP* 2.7 42.5 + + - -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 3.3 32.0 - - + +
88B ASN* 3.9 12.7 + - + -
89B ALA* 3.6 14.4 - - + +
92B THR* 5.5 0.4 - - - +
145B PRO 2.8 18.8 + - - +
146B GLY 3.6 5.8 - - - +
148B TYR* 1.3 76.7 - - - +
150B ARG* 1.3 63.0 + - - +
152B PHE* 3.4 9.7 + - - +
153B LEU* 3.1 21.3 + - - +
162B LEU* 4.7 4.7 - - - +
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 5.3 1.4 - - - +
85B ILE* 3.5 32.4 - - + +
117B TYR* 5.9 0.2 - - - +
118B ASP* 2.6 36.2 + - - +
121B PHE* 3.2 62.2 - - + +
122B ASN* 4.7 8.5 + - - -
146B GLY 3.1 13.8 + - - +
147B VAL* 3.9 4.9 - - - +
149B ALA* 1.3 76.1 - - - +
151B ALA* 1.3 62.1 + - - +
153B LEU* 3.1 4.8 + - - +
154B GLU* 2.8 50.6 + - + +
451B LEU* 3.8 21.7 + - + +
455B ARG* 5.0 4.0 - - - +
462B LEU 5.4 0.4 - - - -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 3.0 18.4 + - + +
148B TYR 3.6 4.9 - - - +
150B ARG* 1.3 77.2 - - - +
152B PHE* 1.3 56.9 + - - +
154B GLU* 3.2 12.7 + - - -
155B GLY 3.1 3.8 + - - -
156B ARG* 2.7 44.5 + - + +
157B LEU* 3.7 22.2 - - + -
186B PHE* 3.8 18.6 - - + -
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ASN* 3.5 28.9 - - - -
148B TYR 3.0 17.6 + - - +
149B ALA 3.5 3.1 - - - +
151B ALA* 1.3 75.7 - - - +
153B LEU* 1.3 61.0 + - + +
155B GLY* 2.8 21.1 + - - -
157B LEU* 3.3 27.9 - - + +
158B THR* 3.9 5.6 - - - -
159B GLN* 3.8 25.8 - - + -
162B LEU* 3.5 25.8 - - + -
438B TYR* 4.0 21.3 - + + -
439B ILE 3.7 1.1 - - - -
440B THR* 3.3 36.1 - - + +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 4.1 12.1 - - + +
84B ALA* 4.2 4.3 - - + -
85B ILE* 3.5 29.4 - - + -
88B ASN* 3.2 16.2 - - - +
149B ALA 3.1 9.5 + - - +
150B ARG* 3.3 9.6 - - - +
152B PHE* 1.3 78.6 - - + +
154B GLU* 1.3 59.1 + - - +
155B GLY 3.1 0.8 + - - -
439B ILE 3.0 31.2 - - - +
440B THR* 4.0 10.3 - - - +
441B PHE* 3.5 39.5 + - + +
448B HIS* 5.2 4.3 - - - -
451B LEU* 3.4 20.5 - - + +
452B HIS* 4.4 3.3 - - - -
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PHE* 4.9 1.6 - - - -
150B ARG* 2.8 43.8 + - + +
151B ALA* 3.5 11.4 - - - +
152B PHE 3.1 0.2 - - - -
153B LEU* 1.3 76.0 - - - +
155B GLY* 1.3 61.2 + - - +
156B ARG* 3.0 35.6 + - + +
451B LEU* 4.0 16.6 - - + -
452B HIS* 3.3 23.8 + - - -
455B ARG* 3.7 15.2 - - - +
461B TYR* 3.4 34.0 - - + +
462B LEU 4.9 1.6 + - - +
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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