Contacts of the helix formed by residues 130 - 140 (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 ASP 130 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440E MET* 5.9 1.3 - - - -
79F TRP* 5.1 2.7 - - + -
80F MET* 4.1 13.8 + - + +
102F HIS* 5.0 9.9 - - + -
104F ALA* 3.7 33.7 - - + +
126F SER* 3.1 22.4 + - - +
128F HIS 2.5 4.6 + - - -
129F GLY* 1.3 70.7 - - - +
131F ARG* 1.3 62.7 + - + +
132F GLU 3.2 0.7 - - - -
133F TYR* 2.8 28.4 + - - +
134F ALA* 3.1 5.7 + - - +
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Residues in contact with ARG 131 (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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332E ASP* 4.9 12.2 + - - -
335E LEU* 4.6 10.1 - - - +
344E ILE* 5.4 6.1 - - - +
432E LEU* 5.3 7.1 - - - +
435E GLY 4.9 2.8 + - - -
436E ALA* 3.7 33.4 - - - +
439E TRP* 4.1 31.8 - - + +
440E MET* 4.9 14.0 - - + +
444E GLY 4.1 8.7 - - - +
445E GLY* 4.4 12.6 - - - -
446E HIS* 4.6 9.2 - - - +
126F SER 5.0 0.8 + - - +
127F ALA* 3.2 37.9 + - - +
128F HIS* 2.5 12.0 + - - +
130F ASP* 1.3 75.9 - - + +
132F GLU* 1.3 52.9 + - - +
134F ALA* 2.7 35.1 + - - +
135F TYR* 3.4 4.7 + - - +
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Residues in contact with GLU 132 (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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188E VAL* 3.1 29.1 - - - +
189E ALA* 3.2 14.9 + - - +
190E VAL* 3.1 41.3 - - - +
445E GLY* 5.2 2.4 - - - -
446E HIS* 4.1 8.1 + - + +
83F PHE* 3.8 15.5 - - + -
84F SER 3.8 18.2 - - - +
85F PRO* 4.1 0.2 - - - +
86F ALA* 3.6 20.5 + - - +
128F HIS 2.6 19.0 + - - +
129F GLY* 4.0 7.9 - - - +
131F ARG* 1.3 68.4 - - - +
133F TYR* 1.3 63.8 + - - +
134F ALA 3.1 0.2 - - - -
135F TYR* 4.0 9.5 + - - +
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Residues in contact with TYR 133 (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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78F THR* 5.6 7.2 - - - -
80F MET* 4.2 17.9 - - + -
84F SER 5.0 2.0 + - - +
86F ALA* 4.3 7.6 - - - -
89F TRP* 4.7 22.7 - + - -
93F THR* 6.1 0.9 - - - -
100F LEU* 6.2 4.0 - - + -
102F HIS* 5.7 9.0 - + + -
129F GLY 3.4 12.1 + - - +
130F ASP* 2.8 15.3 + - - +
132F GLU* 1.3 79.4 - - - +
134F ALA* 1.3 57.3 + - - +
136F ILE* 3.2 16.7 - - + +
137F ASN* 3.0 26.8 + - + +
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Residues in contact with ALA 134 (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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440E MET* 3.3 39.3 - - + +
441E LYS* 5.2 1.1 - - - -
443E GLY* 5.0 0.7 - - - -
444E GLY 5.2 2.0 - - - +
102F HIS* 5.7 5.2 - - + -
130F ASP 3.1 6.4 + - - +
131F ARG* 2.7 19.6 + - - +
133F TYR* 1.3 75.3 - - - +
135F TYR* 1.3 68.9 + - - +
137F ASN* 4.0 8.2 - - + +
138F SER* 2.7 25.1 + - - -
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Residues in contact with TYR 135 (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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196A VAL* 6.1 0.7 - - + -
189E ALA* 4.9 3.8 - - + -
190E VAL* 3.3 41.7 - - + -
394E SER* 5.1 11.0 - - - -
395E TYR 5.2 7.9 - - - -
396E PHE* 6.1 2.9 - + - -
443E GLY* 4.5 13.8 - - - -
444E GLY 4.7 4.3 + - - +
131F ARG 3.4 5.7 + - - -
132F GLU 4.2 4.5 - - - +
133F TYR 3.5 0.4 - - - -
134F ALA* 1.3 80.0 - - - +
136F ILE* 1.3 62.8 + - + +
138F SER* 3.4 1.6 - - - -
139F ARG* 2.7 42.0 + - + +
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Residues in contact with ILE 136 (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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196A VAL* 4.0 27.1 - - + -
200A ILE* 5.0 1.8 - - + -
189E ALA* 4.2 16.4 - - + -
86F ALA* 3.6 36.8 - - + +
89F TRP* 4.0 20.0 - - + -
90F ILE* 3.6 18.8 - - + -
93F THR* 4.6 10.6 - - - +
132F GLU 4.3 0.2 + - - -
133F TYR* 3.2 18.0 + - + +
134F ALA 3.3 0.2 - - - -
135F TYR* 1.3 83.5 - - + +
137F ASN* 1.3 58.4 + - + +
139F ARG* 4.0 12.8 - - + -
140F LEU* 3.6 26.4 - - + +
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Residues in contact with ASN 137 (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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441E LYS* 5.7 5.6 - - + -
93F THR* 5.3 2.9 - - - +
100F LEU* 5.0 11.9 - - + -
102F HIS* 6.5 0.9 - - + -
133F TYR* 3.0 21.2 + - + +
134F ALA* 3.1 8.0 + - - +
136F ILE* 1.3 78.4 - - + +
138F SER* 1.3 57.3 + - - +
139F ARG 3.3 0.2 - - - -
140F LEU 4.1 0.3 - - - -
141F ASN 3.5 1.9 + - - -
142F VAL* 2.8 51.1 + - + +
144F ALA* 6.1 1.6 - - + -
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Residues in contact with SER 138 (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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396E PHE* 6.1 2.5 - - - -
441E LYS* 3.6 32.5 - - - +
442E TYR* 4.3 1.8 - - - -
443E GLY* 3.7 20.4 - - - -
134F ALA 2.7 17.5 + - - -
135F TYR 3.7 1.8 - - - -
137F ASN* 1.3 76.6 - - - +
139F ARG* 1.3 58.0 + - - -
140F LEU 3.5 0.2 - - - -
141F ASN* 3.7 14.6 + - - +
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Residues in contact with ARG 139 (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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194A ASP* 3.4 23.0 + - - -
196A VAL* 4.2 13.4 - - + +
197A ALA* 3.5 23.4 - - - +
200A ILE* 3.9 22.3 - - + +
395E TYR* 2.5 34.9 + - - +
396E PHE* 3.9 23.2 - - + +
397E ASP* 3.3 32.3 - - - +
135F TYR* 2.7 31.4 + - + +
136F ILE* 4.0 13.5 - - + -
137F ASN 3.3 0.4 - - - -
138F SER* 1.3 71.0 - - - +
140F LEU* 1.3 57.9 + - - +
141F ASN* 3.1 12.8 + - - -
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Residues in contact with LEU 140 (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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200A ILE* 3.7 30.3 - - + -
90F ILE* 4.9 4.5 - - + +
93F THR* 5.3 5.2 - - - -
94F GLU* 3.9 32.8 - - + +
136F ILE* 3.6 25.3 + - + +
137F ASN 4.8 1.1 - - - +
139F ARG* 1.3 76.5 - - + +
141F ASN* 1.3 71.9 + - - +
142F VAL* 3.5 5.8 + - + +
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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