Contacts of the strand formed by residues 284 - 290 (chain A) in PDB entry 3ETL
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 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.3 19.7 - - + -
96A GLU* 3.4 42.6 - - + -
99A SER* 4.2 12.8 - - - -
100A VAL 3.3 4.1 + - - +
101A THR* 3.3 21.8 - - + +
102A GLU* 2.8 27.8 + - - +
282A ALA* 4.4 1.2 - - - +
283A THR* 1.3 98.9 - - + +
285A ARG* 1.3 64.5 + - - +
286A PHE* 4.5 6.3 - - + -
300A LEU* 4.4 9.0 - - + -
302A ASP 3.3 4.3 - - - +
303A SER* 3.9 19.3 - - - -
304A PRO* 4.4 4.7 - - + -
305A HIS* 3.9 12.3 - + - -
306A LEU* 4.0 22.4 - - + -
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Residues in contact with ARG 285 (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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102A GLU* 3.6 17.3 + - - +
280A HIS* 2.7 37.2 + - - +
281A ALA* 3.9 3.8 + - - +
282A ALA* 3.4 36.3 + - + +
284A PHE* 1.3 78.4 - - - +
286A PHE* 1.3 61.9 + - - +
300A LEU* 3.5 7.2 - - - +
301A TYR* 3.0 56.7 + - + +
302A ASP* 2.8 44.3 + - + +
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Residues in contact with PHE 286 (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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87A LEU* 3.8 20.2 - - + -
90A VAL* 4.3 6.3 - - + -
91A LEU* 3.3 38.6 - - + -
101A THR* 4.2 9.6 - - - -
102A GLU 2.9 15.6 + - - +
103A PHE* 3.4 44.0 - + + -
104A ALA* 2.9 31.5 + - - +
284A PHE* 4.5 4.3 - - + -
285A ARG* 1.3 76.3 - - - +
287A PHE* 1.3 59.3 + - - +
288A LEU* 4.3 4.9 - - + -
298A ALA* 4.2 12.1 - - + -
299A LYS 3.2 6.5 - - - -
300A LEU* 3.8 41.5 - - + -
301A TYR* 3.6 6.7 - - - -
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Residues in contact with PHE 287 (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 ALA* 3.3 16.4 - - + -
105A GLY* 5.1 1.6 - - - -
258A VAL* 4.8 13.9 - - + -
286A PHE* 1.3 73.7 - - - +
288A LEU* 1.3 63.5 + - - +
289A ARG* 4.5 9.6 - - + +
297A VAL 3.5 2.1 - - - +
298A ALA* 3.4 2.3 - - - -
299A LYS* 2.8 49.0 + - + +
301A TYR* 3.7 50.3 - + + -
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Residues in contact with LEU 288 (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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103A PHE* 3.5 30.5 - - + -
104A ALA 2.7 15.0 + - - +
105A GLY* 3.6 10.4 - - - -
106A MET* 4.2 3.5 + - - +
109A SER* 3.6 29.8 - - - +
110A GLY 3.8 8.3 - - - -
111A LYS* 3.7 36.6 - - + +
114A ILE* 3.9 16.4 - - + -
286A PHE* 4.3 2.5 - - + -
287A PHE* 1.3 75.8 - - - +
289A ARG* 1.3 63.1 + - - +
296A ARG* 5.9 0.4 - - + -
297A VAL 3.4 4.3 - - - +
298A ALA* 3.6 24.0 - - + -
313A PHE* 4.5 8.3 - - + -
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Residues in contact with ARG 289 (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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109A SER* 4.4 2.4 + - - -
287A PHE* 4.5 10.1 - - + +
288A LEU* 1.3 81.4 - - - +
290A LYS* 1.3 73.0 + - - +
291A SER* 5.8 1.4 - - - -
296A ARG* 3.5 6.8 - - - +
297A VAL* 2.9 76.8 + - - +
299A LYS* 5.3 6.2 - - + +
310A GLU* 4.6 12.1 + - - -
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Residues in contact with LYS 290 (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 MET* 6.1 2.7 - - - -
107A PHE* 3.2 51.7 - - - -
108A GLY* 3.7 24.2 - - - +
109A SER* 4.2 5.6 - - - +
289A ARG* 1.3 87.3 + - - +
291A SER* 1.3 65.4 + - - +
296A ARG* 3.8 24.2 - - - +
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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