Contacts of the helix formed by residues 161 - 174 (chain F) in PDB entry 4LQL
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 ALA 161 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LYS 3.9 5.2 - - - +
44F LEU* 3.4 43.9 - - + +
45F ASP* 4.2 9.0 - - - -
157F GLN 3.7 11.4 + - - +
158F GLU* 4.8 4.3 - - - +
159F GLN 3.1 0.4 - - - -
160F ILE* 1.3 77.3 - - - +
162F ASP* 1.3 67.8 + - - +
164F GLN* 3.2 18.7 - - - +
165F HIS* 3.5 6.1 + - - -
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Residues in contact with ASP 162 (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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158F GLU 3.8 7.5 + - - +
159F GLN* 3.0 26.7 + - + +
161F ALA* 1.3 76.6 - - - +
163F TRP* 1.3 59.3 + - - +
164F GLN 2.9 9.3 + - - -
165F HIS* 2.9 18.0 + - - +
166F VAL* 3.3 8.3 + - - +
457F GLU 5.9 0.2 - - - -
458F GLN* 3.2 36.1 - - - +
461F GLN* 4.0 9.6 - - - -
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Residues in contact with TRP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F PHE* 5.0 6.3 - + - -
75F GLY* 4.7 4.3 - - - -
76F VAL 3.7 11.2 - - - -
77F ILE* 4.2 9.4 - - + -
99F PRO* 3.2 34.3 - - + +
100F LEU 3.0 24.0 + - - -
101F LEU* 3.4 43.1 - - + -
144F ALA* 5.7 0.2 - - - +
145F ALA* 3.5 30.8 - - + +
159F GLN 2.8 18.5 + - - +
160F ILE* 4.3 9.9 - - + +
162F ASP* 1.3 73.8 - - - +
164F GLN* 1.3 66.8 + - + +
165F HIS 3.4 0.4 - - - -
166F VAL* 3.8 15.9 - - + -
167F ALA* 3.3 21.5 + - + +
461F GLN* 3.5 25.9 + - + +
465F LEU* 5.7 3.0 - - - +
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Residues in contact with GLN 164 (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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9F PHE* 5.1 14.8 - - + -
44F LEU* 4.6 9.4 - - + -
45F ASP* 5.0 0.2 - - - -
46F TYR* 3.3 32.4 - - + -
47F PRO 6.0 0.4 - - - +
48F VAL* 6.2 0.7 - - + -
77F ILE* 6.5 0.2 - - + -
160F ILE* 3.3 20.0 + - + +
161F ALA* 3.2 18.1 + - - +
162F ASP 2.9 1.4 + - - -
163F TRP* 1.3 87.8 - - + +
165F HIS* 1.3 60.1 + - - +
167F ALA* 3.5 8.5 + - - +
168F VAL* 3.0 26.4 + - - +
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Residues in contact with HIS 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F MET* 5.0 12.6 - - + -
45F ASP* 4.1 23.8 - - - -
46F TYR* 6.1 0.2 - + - -
161F ALA 3.5 2.9 + - - -
162F ASP* 2.9 9.4 + - - +
164F GLN* 1.3 75.4 - - - +
166F VAL* 1.3 57.7 + - - +
167F ALA 2.8 11.2 + - - -
168F VAL* 3.3 15.2 + - - +
169F ALA* 3.4 12.5 + - - +
320F ILE 5.5 1.6 - - - +
321F ALA* 5.0 27.1 - - + +
323F ASP* 5.4 9.4 - - + -
454F LEU* 6.1 3.6 - - + -
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Residues in contact with VAL 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F ASP 3.3 5.3 + - - +
163F TRP* 3.6 23.8 - - + +
165F HIS* 1.3 76.4 - - - +
167F ALA* 1.3 61.2 + - - +
169F ALA* 3.9 6.1 + - - +
170F TYR* 4.0 3.3 + - - +
454F LEU* 6.1 2.6 - - + +
458F GLN* 3.3 33.0 - - + +
461F GLN* 3.5 26.8 - - + +
462F LEU* 3.8 32.1 - - + +
465F LEU* 6.1 0.9 - - - +
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Residues in contact with ALA 167 (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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74F ALA 3.5 18.6 - - - +
75F GLY* 5.1 0.7 - - - -
99F PRO* 3.7 22.9 - - + +
163F TRP* 3.3 23.7 + - + +
164F GLN* 3.8 7.4 - - - +
165F HIS 2.8 0.8 + - - -
166F VAL* 1.3 76.7 - - - +
168F VAL* 1.3 55.8 + - + +
169F ALA 2.6 15.7 + - - -
170F TYR* 2.7 19.1 + - - +
171F ASN* 3.1 12.2 + - - -
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Residues in contact with VAL 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LYS* 5.5 2.9 - - + -
4F MET* 4.3 23.6 - - + -
7F TYR* 3.4 50.0 - - + -
8F LYS 5.9 1.1 - - - +
46F TYR* 5.6 7.4 - - + -
74F ALA* 4.5 5.4 + - + -
164F GLN 3.0 19.7 - - - +
165F HIS* 3.9 5.8 - - - +
167F ALA* 1.3 74.8 - - + +
169F ALA* 1.3 58.9 + - - +
171F ASN* 3.4 11.9 - - - +
172F GLU* 2.8 26.4 + - + +
320F ILE* 6.1 2.9 - - + +
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Residues in contact with ALA 169 (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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165F HIS 3.4 11.4 + - - +
166F VAL* 4.1 7.2 - - - +
167F ALA 2.6 6.5 + - - -
168F VAL* 1.3 74.6 - - - +
170F TYR* 1.3 60.0 + - - +
171F ASN 3.1 1.1 - - - -
172F GLU* 2.8 6.0 + - - +
173F SER* 2.7 38.9 + - - +
317F LEU* 4.2 18.8 - - + +
320F ILE* 5.1 10.3 - - + -
321F ALA* 5.8 4.7 - - + +
462F LEU* 4.7 11.0 - - + -
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Residues in contact with TYR 170 (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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99F PRO* 5.6 10.1 - - + -
166F VAL 4.0 6.5 + - - +
167F ALA* 2.7 13.0 + - - +
169F ALA* 1.3 73.7 - - - +
171F ASN* 1.3 63.9 + - - +
173F SER* 3.9 7.7 + - - -
174F PHE* 3.8 22.5 + + - +
462F LEU* 4.9 7.9 - - + +
465F LEU* 3.7 40.4 - - + -
466F PHE* 4.5 13.7 - + - -
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Residues in contact with ASN 171 (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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7F TYR* 3.8 17.7 - - + -
73F VAL 4.9 2.0 - - - -
74F ALA* 3.3 44.0 - - - -
98F LYS* 5.2 6.1 - - - -
99F PRO* 5.1 7.6 - - - +
167F ALA 3.1 10.7 + - - -
168F VAL* 3.4 9.4 - - - +
170F TYR* 1.3 80.4 - - - +
172F GLU* 1.3 61.9 + - - +
174F PHE* 3.8 4.9 + - - +
175F HIS* 3.6 22.9 + - - -
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Residues in contact with GLU 172 (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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3F LYS* 5.2 5.4 - - + -
7F TYR* 3.5 21.8 - - + +
168F VAL* 2.8 18.9 + - + +
169F ALA* 2.8 9.1 + - - +
171F ASN* 1.3 77.7 - - - +
173F SER* 1.3 62.8 + - - +
175F HIS* 3.1 24.4 + - + +
176F ILE* 3.3 7.8 + - + +
320F ILE* 4.0 26.2 - - + -
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Residues in contact with SER 173 (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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169F ALA* 2.7 31.2 + - - +
170F TYR* 4.3 6.2 - - - -
172F GLU* 1.3 66.7 - - - +
174F PHE* 1.3 55.9 + - - +
175F HIS 2.4 18.2 + - - -
176F ILE* 2.5 25.6 + - - +
202F LEU* 3.5 20.8 - - - +
203F GLY 3.7 9.5 - - - +
204F TRP* 5.7 0.2 - - - -
317F LEU* 4.0 26.4 - - - +
466F PHE* 5.9 4.5 - - - -
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Residues in contact with PHE 174 (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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91A ARG* 4.4 27.2 - - + +
170F TYR* 3.8 20.4 - + - +
171F ASN 3.8 5.9 + - - +
172F GLU 3.3 0.8 - - - -
173F SER* 1.3 75.7 - - - +
175F HIS* 1.4 65.0 + - + +
201F LYS 6.0 0.7 - - - -
202F LEU 4.6 2.7 - - - -
203F GLY* 4.1 29.7 - - - +
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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