Contacts of the strand formed by residues 270 - 278 (chain A) in PDB entry 5JQE
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 PHE 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU 3.9 3.8 - - - +
124A ALA* 4.1 6.2 - - - -
125A LEU* 4.4 3.0 - - - +
167A TYR* 3.6 46.3 + + + -
170A TRP* 3.2 49.8 - + + -
171A PRO* 5.2 0.6 - - - +
180A ALA* 4.8 1.8 - - + -
268A LYS 4.0 0.4 + - - -
269A PRO* 1.3 74.8 - - - +
271A VAL* 1.3 60.6 - - - +
340A GLU* 3.3 27.6 - - + -
342A MET* 4.0 21.5 - - + -
343A PRO* 4.4 12.3 - - + -
348A MET* 4.9 1.6 - - + -
351A PHE* 3.5 26.0 - + - -
352A TRP* 3.6 30.5 - + - -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.2 18.2 - - - -
104A PHE* 4.5 7.2 - - + -
122A VAL* 3.7 23.8 - - + -
123A GLU 3.4 11.0 - - - +
124A ALA* 4.5 2.5 - - + -
269A PRO 3.7 13.2 - - - +
270A PHE* 1.3 72.1 - - - +
272A GLY* 1.3 64.0 + - - +
273A VAL* 4.4 9.0 - - + -
336A ALA* 3.3 37.7 - - + +
339A GLY* 4.0 1.1 - - - -
340A GLU 2.9 20.1 + - - +
341A ILE* 4.0 10.7 - - + +
342A MET* 3.3 14.9 + - - +
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Residues in contact with GLY 272 (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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75A ALA* 6.0 2.9 - - - -
76A HIS* 3.8 6.3 - - - -
77A ASP* 5.6 2.2 - - - -
122A VAL* 3.4 3.8 - - - -
123A GLU* 2.8 46.1 + - - +
167A TYR* 5.4 1.8 + - - -
270A PHE 4.0 1.6 + - - -
271A VAL* 1.3 73.9 - - - +
273A VAL* 1.3 62.5 + - - +
274A LEU 4.1 1.2 + - - -
342A MET* 4.9 8.4 - - - +
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Residues in contact with VAL 273 (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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75A ALA* 3.6 3.4 - - - +
76A HIS* 2.9 41.7 + - + +
104A PHE* 5.6 0.4 - - + -
105A THR* 4.8 10.1 - - + +
108A ALA* 3.7 25.6 - - + -
109A VAL* 5.4 0.2 - - + -
119A PRO* 3.8 22.9 - - + -
121A ALA 3.2 16.2 - - - +
122A VAL* 4.6 10.3 - - + -
271A VAL* 4.4 13.0 - - + +
272A GLY* 1.3 75.5 - - - +
274A LEU* 1.3 65.1 + - - +
275A SER* 3.1 18.9 + - - +
341A ILE* 4.9 5.8 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 5.5 3.8 - - + -
27A LYS* 4.1 39.7 - - + +
73A PHE* 4.1 17.5 - - + +
74A TRP* 3.6 30.5 - - - +
75A ALA* 4.3 2.9 - - - +
120A ILE* 2.8 44.9 + - + +
121A ALA* 3.1 24.1 + - + -
272A GLY 4.1 1.4 - - - -
273A VAL* 1.3 72.1 - - - +
275A SER* 1.3 62.8 + - - +
311A LEU* 4.4 20.4 - - + -
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Residues in contact with SER 275 (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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73A PHE* 3.3 4.3 - - - -
74A TRP 2.8 34.2 + - - +
76A HIS* 3.8 4.9 - - - +
79A PHE* 3.4 12.6 - - - -
109A VAL* 3.8 11.5 - - - +
117A ALA* 3.7 19.3 - - - -
118A TYR 3.2 14.8 + - - -
119A PRO* 4.2 0.2 - - - +
120A ILE* 4.0 3.8 - - - -
273A VAL* 3.1 25.7 + - - +
274A LEU* 1.3 75.7 + - - +
276A ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 276 (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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71A ILE* 3.9 4.3 - - + -
72A ILE 3.3 4.3 - - - -
73A PHE* 3.5 38.4 - - + -
117A ALA* 3.3 2.9 - - - -
118A TYR* 2.9 41.4 + - + +
120A ILE* 3.9 5.1 - - + +
275A SER* 1.3 70.5 - - - +
277A GLY* 1.3 60.9 + - - +
292A LEU* 3.6 20.7 - - + +
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Residues in contact with GLY 277 (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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71A ILE* 3.4 7.6 - - - +
72A ILE* 2.9 35.1 + - - +
79A PHE* 3.5 4.7 - - - -
88A LEU* 3.6 21.1 - - - -
116A ILE 4.2 0.9 - - - -
117A ALA* 3.9 14.4 - - - -
276A ALA* 1.3 74.8 - - - +
278A ILE* 1.3 63.1 + - - -
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Residues in contact with ILE 278 (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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70A ASP 3.6 7.4 - - - +
71A ILE* 4.9 1.1 - - + -
88A LEU* 3.3 10.0 - - - +
89A ALA* 3.1 27.3 + - + +
91A ILE* 3.7 28.9 - - + -
116A ILE 4.4 5.7 + - - -
118A TYR* 4.0 13.7 - - + -
277A GLY* 1.3 75.8 - - - +
279A ASN* 1.3 75.3 + - - +
282A SER* 5.2 1.8 - - - -
285A LYS* 4.0 30.5 - - + +
288A ALA* 4.2 16.8 - - + -
289A LYS* 4.2 20.6 - - + -
292A LEU* 4.2 14.8 - - + -
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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