Contacts of the helix formed by residues 130 - 141 (chain L) in PDB entry 1XFB
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 GLY 130 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126K GLN* 3.1 18.4 + - - +
128L LEU 3.1 2.6 + - - -
129L ASP* 1.3 70.5 - - - +
131L LEU* 1.3 64.8 + - - +
132L SER 3.2 3.4 - - - -
133L GLU* 3.1 24.4 + - - +
134L ARG* 3.1 25.8 + - - +
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Residues in contact with LEU 131 (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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109L VAL* 3.6 33.4 - - + +
127L GLY 3.7 7.2 - - - +
128L LEU* 3.1 21.3 + - + +
129L ASP 3.1 4.4 + - - -
130L GLY* 1.3 76.8 - - - +
132L SER* 1.3 57.5 + - - +
134L ARG* 3.2 21.3 + - + +
135L CYS* 2.8 43.8 + - - -
148L TRP* 4.4 4.9 - - + -
174L TYR* 4.0 29.6 - - + +
177L ILE* 4.0 29.6 - - + -
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Residues in contact with SER 132 (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 LEU 4.9 0.2 + - - -
130L GLY 3.1 1.0 + - - -
131L LEU* 1.3 77.9 - - - +
133L GLU* 1.3 74.2 + - - +
135L CYS 3.3 0.7 + - - -
136L ALA* 3.0 20.6 + - - +
177L ILE* 3.5 20.5 - - - +
180L GLN* 3.5 14.5 + - - -
181L ASN* 2.9 29.7 + - - +
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Residues in contact with GLU 133 (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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126K GLN* 5.2 4.0 + - - +
130L GLY* 3.1 27.8 + - - +
132L SER* 1.3 85.0 + - - +
134L ARG* 1.3 65.3 + - + +
136L ALA* 3.3 9.3 + - - +
137L GLN* 3.0 23.7 + - - +
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Residues in contact with ARG 134 (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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108L LYS 4.5 1.8 + - - -
109L VAL* 3.0 41.1 + - - +
110L ASP 5.1 0.2 + - - -
111L LYS* 3.7 25.1 - - - +
127L GLY 3.4 20.0 + - - -
129L ASP 4.4 3.8 - - - -
130L GLY 3.1 19.5 + - - +
131L LEU* 3.5 16.4 - - + +
133L GLU* 1.3 75.8 - - + +
135L CYS* 1.3 61.3 + - - +
137L GLN* 3.1 8.2 + - - +
138L TYR* 2.8 63.7 + - + +
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Residues in contact with CYS 135 (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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107L ILE* 6.5 0.2 - - - -
109L VAL* 5.1 6.7 - - - -
131L LEU* 2.8 47.9 + - - +
132L SER 3.7 4.3 - - - +
134L ARG* 1.3 68.7 - - - +
136L ALA* 1.3 70.0 + - - +
137L GLN 3.0 0.3 + - - -
138L TYR* 3.0 6.0 + - - +
139L LYS* 2.8 26.3 + - - +
146L ALA* 5.7 0.2 - - - -
177L ILE* 4.8 0.4 - - - -
178L CYS* 4.0 30.3 - - - -
181L ASN* 3.7 20.9 - - + +
183L ILE* 3.6 17.6 - - + +
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Residues in contact with ALA 136 (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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132L SER 3.0 10.0 + - - +
133L GLU* 3.4 12.3 - - - +
135L CYS* 1.3 77.3 - - - +
137L GLN* 1.3 55.9 + - - +
139L LYS* 3.6 6.8 + - - +
140L LYS* 3.1 36.9 + - - +
181L ASN* 3.5 20.8 + - - +
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Residues in contact with GLN 137 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85L TYR* 4.6 1.8 + - - +
133L GLU 3.0 13.0 + - - +
134L ARG* 3.3 11.2 - - - +
136L ALA* 1.3 75.4 - - - +
138L TYR* 1.3 70.3 + - + +
140L LYS* 2.9 36.9 + - - +
141L ASP* 2.9 51.0 + - - +
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Residues in contact with TYR 138 (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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81L HIS* 2.6 45.1 + + - +
84L LEU* 3.7 15.0 - - + +
85L TYR* 3.6 15.7 - - - -
107L ILE* 3.8 36.5 - - + +
108L LYS 4.9 1.3 + - - -
109L VAL* 4.0 22.4 - - + -
134L ARG* 2.8 58.2 + - + +
135L CYS* 3.6 6.7 - - - +
137L GLN* 1.3 76.5 - - + +
139L LYS* 1.3 62.6 + - - +
141L ASP* 2.9 14.7 + - - +
142L GLY 3.2 0.7 + - - -
143L ALA* 3.0 22.4 + - + +
183L ILE* 4.5 1.8 - - + -
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Residues in contact with LYS 139 (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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15L GLU* 2.9 29.9 + - - -
19L ILE* 3.7 5.7 - - - +
135L CYS 2.8 20.5 + - - +
136L ALA* 3.6 6.3 - - - +
138L TYR* 1.3 72.2 - - - +
140L LYS* 1.3 59.9 + - - +
142L GLY* 2.9 22.0 + - - -
143L ALA 3.2 20.5 + - - +
144L ASP* 2.9 21.9 + - - +
181L ASN 4.0 10.1 - - - +
182L GLY* 2.7 33.3 + - - +
183L ILE* 3.9 9.5 - - + +
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Residues in contact with LYS 140 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136L ALA* 3.1 17.8 + - - +
137L GLN* 2.9 36.6 + - - +
139L LYS* 1.3 79.7 - - - +
141L ASP* 1.3 63.4 + - - +
142L GLY 3.4 0.6 + - - -
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Residues in contact with ASP 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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84L LEU* 4.7 8.1 - - + +
85L TYR* 2.6 43.2 + - + +
95L VAL* 3.8 19.4 - - - +
137L GLN* 2.9 31.1 + - - +
138L TYR* 2.9 11.7 + - - +
140L LYS* 1.3 86.9 - - - +
142L GLY* 1.3 55.6 + - - +
143L ALA 3.7 0.6 + - - -
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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