Contacts of the strand formed by residues 216 - 222 (chain A) in PDB entry 2XXA
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU 4.0 0.3 - - - +
94A ASN* 3.5 31.9 - - + +
95A LEU* 2.9 31.0 + - + +
102A VAL 3.4 3.9 + - - +
103A VAL* 3.3 22.0 - - + +
104A LEU 3.0 26.2 + - - +
214A PRO* 4.0 1.4 - - - +
215A VAL* 1.4 88.9 - - + +
217A THR* 1.3 61.5 + - - +
218A LEU* 3.7 3.7 + - + +
243A THR* 2.9 26.2 - - - +
271A LYS* 3.0 26.4 + - - +
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Residues in contact with THR 217 (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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104A LEU* 3.6 19.3 - - + +
106A ALA* 5.6 4.5 - - + -
209A HIS* 3.1 38.1 + - + +
214A PRO* 3.6 13.9 + - - +
216A GLU* 1.3 70.0 - - - +
218A LEU* 1.3 62.1 + - - +
219A PHE 3.7 0.3 + - - -
240A LEU* 4.7 5.8 - - + -
241A PRO 3.7 17.2 + - - +
242A LEU* 3.6 21.9 - - + +
243A THR* 2.8 31.5 + - - -
244A GLY 3.4 4.7 - - - +
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Residues in contact with LEU 218 (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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94A ASN* 3.9 19.1 - - - +
103A VAL* 3.7 26.9 - - + -
104A LEU 3.0 9.9 + - - +
105A MET* 3.5 28.2 - - + +
106A ALA* 3.2 24.7 + - - +
120A LEU* 4.1 11.4 - - + -
216A GLU* 3.7 3.6 - - + -
217A THR* 1.3 73.1 - - - +
219A PHE* 1.3 59.0 + - - +
220A VAL 3.7 1.1 + - - -
242A LEU* 5.2 1.1 - - - -
243A THR 4.0 3.4 - - - +
244A GLY* 3.4 26.9 - - - -
245A VAL 4.1 0.9 - - - +
246A VAL* 4.0 19.5 - - + -
271A LYS* 4.0 20.9 - - + -
272A PHE* 4.3 2.2 - - + -
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Residues in contact with PHE 219 (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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106A ALA 3.3 16.8 - - - -
107A GLY* 4.2 5.4 - - - -
108A LEU 5.2 0.7 - - - -
217A THR 3.7 0.8 + - - -
218A LEU* 1.3 68.6 - - - +
220A VAL* 1.4 66.1 + - - +
221A VAL* 3.8 21.8 - - + -
232A THR* 3.5 28.0 - - + -
233A ALA* 4.9 4.9 - - - -
236A PHE* 3.5 42.2 - + + -
242A LEU* 3.8 29.6 - - + -
244A GLY 2.9 14.8 + - - +
245A VAL* 3.3 15.5 - - + +
246A VAL 3.0 18.9 + - - -
262A ILE* 3.9 34.1 - - + -
266A THR* 5.3 0.4 - - + -
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Residues in contact with VAL 220 (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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105A MET* 3.7 32.5 - - + -
106A ALA 3.1 7.0 + - - +
107A GLY* 3.6 19.8 - - - -
108A LEU 4.4 1.0 + - - -
111A ALA* 3.7 10.8 - - + +
112A GLY 3.9 16.6 - - - +
113A LYS* 3.8 29.4 - - + +
116A SER* 4.3 1.1 - - - +
218A LEU 4.3 3.4 - - - +
219A PHE* 1.4 74.6 - - - +
221A VAL* 1.3 62.4 + - - +
246A VAL* 3.4 20.2 - - + +
248A THR* 3.9 26.2 - - + +
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Residues in contact with VAL 221 (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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108A LEU* 6.1 2.2 - - + -
111A ALA* 4.2 3.8 - - - -
219A PHE* 3.8 17.7 - - + -
220A VAL* 1.3 74.1 - - - +
222A ASP* 1.3 66.5 + - - +
225A THR* 3.8 21.3 - - + +
229A ALA* 5.6 1.8 - - + -
232A THR* 5.1 6.5 - - + -
245A VAL* 3.9 15.5 - - + -
246A VAL 3.1 5.6 + - - +
247A LEU* 3.6 24.0 - - + +
248A THR* 3.3 24.6 + - - -
258A ALA* 5.4 0.7 - - + -
262A ILE* 3.9 32.8 - - + -
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Residues in contact with ASP 222 (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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110A GLY 4.3 4.2 - - - +
111A ALA* 4.3 10.2 - - + +
221A VAL* 1.3 79.4 - - - +
223A ALA* 1.3 68.5 + - - +
224A MET* 3.3 34.7 + - - +
225A THR* 2.6 43.6 + - + +
247A LEU* 4.8 0.4 - - - +
248A THR* 3.8 7.9 + - - +
249A LYS* 2.9 43.5 + - - +
258A ALA* 4.4 3.5 - - - +
107B ASN 4.5 0.2 - - - +
108B GLY 4.7 2.4 - - - +
225B ASP* 5.5 2.1 - - - +
228B THR* 5.6 0.4 - - - +
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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