Contacts of the helix formed by residues 259 - 271 (chain A) in PDB entry 6LGV
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 ASN 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.0 5.9 - - - +
42A MET* 4.2 10.0 - - - +
102A VAL* 3.5 12.6 - - + +
103A ALA* 3.1 23.0 + - + +
104A SER 3.8 8.3 - - - +
105A GLY* 3.6 2.3 - - - +
106A THR* 4.2 10.9 - - - +
164A VAL* 5.5 0.3 - - - +
258A GLN* 1.3 67.3 - - - +
260A SER* 1.3 58.9 + - - +
262A LEU* 3.0 34.2 - - + +
263A ALA 3.1 16.5 + - - -
401A CIT 2.7 54.3 + - - +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.8 1.1 - - - -
258A GLN* 2.9 9.0 + - - -
259A ASN* 1.3 70.9 - - - +
261A GLY* 1.3 60.8 + - - +
263A ALA* 3.5 9.3 - - - +
264A ALA* 2.8 30.5 + - - +
279A GLY* 3.5 19.9 - - - +
282A PHE* 3.8 21.5 - - - -
283A SER* 3.3 16.1 + - - -
286A HIS* 3.2 25.1 - - - -
401A CIT 3.0 3.2 + - - -
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.7 1.3 - - - +
38A LEU* 3.6 13.5 - - - -
200A ILE* 4.4 9.0 - - - -
204A VAL* 5.5 0.7 - - - -
260A SER* 1.3 74.6 - - - +
262A LEU* 1.3 60.2 + - - +
264A ALA* 3.4 5.3 + - - +
265A THR* 2.9 28.8 + - - -
283A SER* 4.1 1.6 - - - -
401A CIT 2.9 33.4 + - - -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.7 8.5 - - + +
102A VAL* 4.5 12.1 - - + -
103A ALA* 5.7 4.9 - - + +
137A THR* 6.1 0.7 - - + +
160A ILE* 4.5 13.7 - - + -
163A ILE* 4.1 35.9 - - + -
164A VAL* 3.8 24.0 - - + -
259A ASN* 3.0 34.5 - - + +
261A GLY* 1.3 74.4 - - - +
263A ALA* 1.3 56.7 + - - +
265A THR* 3.2 2.6 + - - -
266A LEU* 2.8 61.9 + - + +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.7 14.0 - - + +
99A VAL* 3.7 41.7 - - + +
102A VAL* 3.9 10.2 - - + +
259A ASN 3.1 8.8 + - - +
260A SER* 3.5 17.3 - - - +
262A LEU* 1.3 76.0 - - - +
264A ALA* 1.3 57.6 + - - +
266A LEU* 4.9 2.0 - - - -
267A GLY* 2.9 27.2 + - - -
275A ALA 5.0 2.0 - - - +
279A GLY* 4.9 0.4 - - - -
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 4.4 21.3 - - + -
260A SER 2.8 19.8 + - - +
261A GLY* 3.8 4.7 - - - +
262A LEU 3.3 0.2 - - - -
263A ALA* 1.3 72.9 - - - +
265A THR* 1.3 62.1 + - - +
267A GLY 3.4 0.2 + - - -
268A LYS* 3.0 21.5 + - - +
276A ALA* 3.5 39.9 - - + +
279A GLY* 4.0 2.8 - - - +
280A ALA* 3.9 11.0 - - - +
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.3 24.9 - - + +
35A GLY* 4.9 12.1 - - - +
38A LEU* 3.7 5.9 - - + +
163A ILE* 4.2 19.5 - - + -
204A VAL* 5.7 0.2 - - - +
261A GLY 2.9 20.5 + - - -
262A LEU* 3.7 4.9 - - - -
264A ALA* 1.3 77.1 - - - +
266A LEU* 1.3 62.9 + - - +
268A LYS* 3.3 6.4 + - - +
269A ILE* 3.0 41.9 + - + +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.7 24.1 - - + +
102A VAL* 4.6 5.6 - - + -
137A THR* 4.6 0.9 - - + -
156A MET* 3.9 26.0 - - + -
159A SER* 3.9 28.3 - - - -
160A ILE* 3.9 26.7 - - + +
163A ILE* 5.1 3.1 - - + -
262A LEU* 2.8 43.4 + - + +
263A ALA 4.0 0.2 - - - +
265A THR* 1.3 76.3 - - - +
267A GLY* 1.3 57.4 + - - +
269A ILE* 4.5 3.8 - - + -
270A TYR* 2.9 43.7 + - + +
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Residues in contact with GLY 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.3 16.9 - - - +
263A ALA 2.9 15.1 + - - -
264A ALA 3.4 2.0 + - - -
265A THR 3.2 0.2 - - - -
266A LEU* 1.3 77.0 - - - +
268A LYS* 1.3 57.7 + - - +
271A PHE* 2.8 34.2 + - - +
272A SER 3.2 13.3 + - - -
275A ALA* 4.2 15.3 - - - -
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 4.5 22.6 + - - -
32A PRO* 5.2 1.4 - - - +
264A ALA 3.0 17.0 + - - +
265A THR* 3.8 5.4 - - - +
267A GLY* 1.3 76.1 - - - +
269A ILE* 1.3 66.6 + - + +
271A PHE 4.3 2.9 + - - -
272A SER* 3.7 17.7 + - - +
273A PRO* 4.8 16.7 - - + +
276A ALA* 4.3 11.7 - - + +
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 4.3 17.5 - - - +
163A ILE* 5.1 4.9 - - + -
265A THR* 3.0 37.6 + - + +
266A LEU* 4.8 2.0 - - + -
268A LYS* 1.3 82.8 - - + +
270A TYR* 1.3 97.3 + - + +
271A PHE 3.8 0.7 + - - -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER 4.5 4.9 - - - +
152A ASP* 4.0 34.1 + - + +
155A GLY* 2.7 28.4 + - - -
156A MET* 3.8 31.2 - - + -
159A SER* 2.5 32.7 + - - -
266A LEU* 2.9 27.8 + - + +
269A ILE* 1.3 100.0 - - + +
271A PHE* 1.3 83.4 + - + +
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 5.0 5.8 - - + -
94A ALA* 4.2 17.9 - - + -
98A LEU* 3.8 28.9 - - + -
141A THR* 3.8 17.7 - - + -
149A ILE* 3.3 37.7 - - + -
150A SER 3.5 14.4 - - - -
151A VAL* 3.8 23.8 - - + -
156A MET* 4.7 2.5 - - + -
267A GLY* 2.8 15.6 + - - +
268A LYS 4.6 3.3 - - - +
269A ILE 3.6 1.4 - - - +
270A TYR* 1.3 96.2 - - + +
272A SER* 1.3 65.2 + - - +
275A ALA* 3.7 12.8 - - + -
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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