Contacts of the helix formed by residues 140 - 151 (chain L) in PDB entry 4XLR
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 GLU 140 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138L ASP* 4.4 2.0 - - + +
139L GLN* 1.3 79.7 - - + +
141L LEU* 1.3 66.8 + - - +
142L ILE 3.7 0.4 - - - -
143L ARG* 3.2 37.4 + - - +
144L GLU* 3.3 24.5 + - + +
147L ARG* 4.1 8.7 + - - -
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Residues in contact with LEU 141 (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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137L LEU* 3.7 37.2 - - + -
138L ASP* 3.8 29.3 + - + +
139L GLN 3.4 1.0 - - - -
140L GLU* 1.3 80.0 - - - +
142L ILE* 1.3 68.8 + - + +
143L ARG 3.0 0.7 + - - -
144L GLU* 3.2 3.9 + - - +
145L VAL* 3.0 28.0 + - + +
165L LYS* 5.2 7.3 + - - +
170L THR* 4.1 29.8 - - + +
174L VAL* 4.2 11.0 - - + -
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Residues in contact with ILE 142 (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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128L ILE* 3.7 23.6 - - + +
131L LEU* 3.7 36.6 - - + +
132L SER* 3.8 12.3 - - - +
137L LEU* 3.7 38.4 - - + -
138L ASP 3.9 11.7 - - - +
139L GLN 4.5 0.4 - - - +
141L LEU* 1.3 75.1 - - - +
143L ARG* 1.3 54.4 + - - +
145L VAL* 3.4 10.7 - - + +
146L VAL* 2.7 39.8 + - + +
174L VAL* 3.9 13.2 - - + -
178L LEU* 4.4 8.5 - - + -
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Residues in contact with ARG 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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125L MET* 3.8 25.1 - - - +
128L ILE* 3.7 29.5 - - + +
139L GLN 4.0 8.5 - - - +
140L GLU* 3.2 37.3 + - - +
141L LEU 3.0 0.2 - - - -
142L ILE* 1.3 77.7 - - - +
144L GLU* 1.3 61.7 + - - +
146L VAL* 2.9 30.2 + - - +
147L ARG* 3.2 12.6 + - - +
196L GLU* 3.2 42.8 + - - +
199L ARG* 3.0 46.3 - - - +
240L GLU* 4.7 7.5 + - - +
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Residues in contact with GLU 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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559J ALA* 3.6 22.7 - - - +
560J GLN* 4.9 1.2 - - - -
140L GLU* 3.3 18.0 + - + +
141L LEU 3.2 7.5 + - - +
143L ARG* 1.3 78.6 - - - +
145L VAL* 1.3 57.8 + - - +
147L ARG* 3.1 34.2 + - + +
148L ALA* 3.0 23.0 + - - +
156L ILE* 6.5 0.9 - - + -
157L GLN* 4.5 14.8 + - - +
164L GLU* 3.4 22.3 - - - +
165L LYS* 3.6 21.5 - - - +
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Residues in contact with VAL 145 (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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141L LEU* 3.0 25.8 + - + +
142L ILE* 3.4 16.6 - - + +
144L GLU* 1.3 74.8 - - - +
146L VAL* 1.3 59.5 + - - +
148L ALA* 2.8 24.7 + - - +
149L LYS* 3.2 8.3 + - - +
157L GLN* 5.7 0.2 - - - +
165L LYS* 5.0 5.8 - - - +
171L VAL* 4.4 14.8 - - + -
174L VAL* 4.0 25.1 - - + -
175L ASP* 3.3 31.4 - - - +
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Residues in contact with VAL 146 (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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128L ILE* 4.6 5.8 - - + -
142L ILE* 2.7 31.2 + - + +
143L ARG* 3.1 14.1 - - - +
145L VAL* 1.3 73.2 - - - +
147L ARG* 1.3 56.1 + - - +
148L ALA 3.3 0.3 + - - -
149L LYS* 3.3 1.4 + - - +
150L ILE* 3.0 42.9 + - + +
192L ALA* 4.1 23.3 - - + +
193L ARG* 4.2 20.9 - - + +
196L GLU* 3.2 30.3 - - + +
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Residues in contact with ARG 147 (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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559J ALA 4.7 0.7 - - - +
560J GLN* 2.8 37.8 + - - +
561J GLY* 3.6 18.6 - - - +
140L GLU* 4.1 9.1 + - - -
143L ARG* 3.2 27.5 + - - +
144L GLU* 3.1 39.3 + - + +
146L VAL* 1.3 79.1 - - - +
148L ALA* 1.3 62.7 + - - +
150L ILE* 4.5 0.4 - - - -
151L LEU* 3.0 39.3 + - + +
156L ILE* 4.0 11.1 - - + +
196L GLU* 3.2 20.9 + - - +
199L ARG* 3.1 35.9 - - - +
200L GLN* 5.9 0.7 - - - +
240L GLU* 5.3 1.2 + - - -
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Residues in contact with ALA 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 GLU 3.0 9.3 + - - +
145L VAL* 2.8 20.7 + - - +
147L ARG* 1.3 78.0 - - - +
149L LYS* 1.3 56.0 + - - +
152L GLY 2.9 19.8 - - - +
153L THR 4.5 5.4 - - - +
156L ILE* 4.8 8.1 - - - +
157L GLN* 4.2 11.9 - - - +
167L ASP* 5.5 1.6 - - - +
171L VAL* 4.0 22.0 - - + -
175L ASP* 4.5 4.7 - - - +
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Residues in contact with LYS 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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410J THR* 4.8 2.2 + - + -
411J THR 4.7 2.8 - - - +
412J GLY* 5.4 4.3 - - - -
413J ASP* 4.4 28.7 + - - +
145L VAL 3.2 9.5 + - - +
146L VAL* 3.3 0.6 + - - -
148L ALA* 1.3 75.5 - - - +
150L ILE* 1.3 63.7 + - - +
152L GLY 4.2 5.2 - - - +
175L ASP* 3.3 29.1 + - - +
179L LYS* 3.4 36.0 - - - +
193L ARG* 3.3 38.6 + - - +
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Residues in contact with ILE 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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162J ARG* 5.8 2.3 + - - -
411J THR* 3.3 30.3 - - - +
412J GLY* 5.3 2.7 - - - -
146L VAL* 3.0 33.0 + - + +
147L ARG* 4.5 2.0 - - - -
148L ALA 3.4 0.4 - - - -
149L LYS* 1.3 78.9 - - - +
151L LEU* 1.3 60.4 + - + +
152L GLY* 2.8 17.5 + - - -
193L ARG* 3.3 39.3 - - + +
196L GLU* 5.0 5.4 - - + +
197L ALA* 5.4 13.7 - - + +
200L GLN* 6.4 1.6 - - + -
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Residues in contact with LEU 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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558J LEU 4.5 4.3 - - - +
561J GLY* 3.5 35.4 - - - +
562J ALA 3.6 20.0 - - - +
563J PRO* 5.1 2.0 - - + -
564J GLU* 4.9 19.6 - - + +
567J ILE* 6.2 1.6 - - + -
147L ARG* 3.0 23.5 + - + +
150L ILE* 1.3 79.7 - - + +
152L GLY* 1.3 55.5 + - - +
155L ARG* 4.7 4.7 + - - -
156L ILE* 3.5 35.6 - - + +
200L GLN* 5.1 8.3 - - + +
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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
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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